111 Questions 229 Answers 0 Followers
Questions related from Anthony Nash
Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...
01 January 2020 8,528 5 View
I have a licensed copy of PyMol (ver 2.3.1) and I am looking to 'replicate' a protein/bilayer i.e., in VMD you select "Periodic" and select from a number of x, y and z options. This, in turn,...
12 December 2019 7,768 4 View
I'm waiting on email conformation for the GMX user group, but this is in reply to Reviewers so I'm pressed for time and asking here. I'm building a small collagen-based system. The crystal...
11 November 2019 4,760 8 View
Hi, I know the fundamentals, I'm would like an update on the available open-source software. I have a set of small molecules and drug molecules. I've derived their ground state structure using...
11 November 2019 9,777 3 View
What is the keyword to increase the number of optimisation steps (not the number of SCF steps) in an ORCA optimisation calculation? The warning is suggesting I increase the "number of...
09 September 2019 2,089 2 View
I'm picking up quantum chemistry after a three year break. I've forgot a lot and I'm now using ORCA (version 4.0.1.2). My system is a non-enzymatic chemical reaction between lysine, arginine...
08 August 2019 1,844 3 View
I am looking for an old piece of software called CHI. It was used to model protein transmembrane domain interactions in a gas phase. I believe it was part of...
02 February 2019 5,498 2 View
Hi all. A similar question to this has been asked several times, however there is subtle difference. I would like to change e.g., an alanine to a glycine (or any amino acid) in a .gro file AND...
12 December 2018 888 11 View
Hello all, I have a huge dataset of longitudinal medical records. Each record contains indications for drug and disease. I have been able to calculate the Cure Rate in the population given a...
10 October 2018 2,261 5 View
I am looking for any available tools that will group drugs by their mechanism/mode of action (MOA/MoA)? For example, a list of all drugs that work on the mu opioid receptor, along with some...
09 September 2018 8,782 3 View
I have a longitudinal retrospective data set of human medical records. They feature CONDITION and DRUG. There is no way of saying why a drug was prescribed other than observing the...
09 September 2018 10,204 3 View
I have six time-series plots as a measurement of some soft-matter physical function F(t), see the graph below. In most instances, it is quite clear that particular variations in the property of...
09 September 2018 651 8 View
I have 1600 drugs to treat a condition. I firstly test them each by performing a drug screen. I divide the 1600 drugs into successes and failures. For example: 100 drugs were successful 1500...
07 July 2018 5,336 20 View
In this open access paper: https://bmjopen.bmj.com/content/bmjopen/3/3/e002057.full.pdf In tables 2 and 3, for each model there is a hazard ratio (HR) for the outcome (depression: yes or no) and...
07 July 2018 2,956 3 View
I would appreciate a sanity check of whether I am using Cox PH regression in R correctly to analyse recurrent events. First of all, I am sorry for the formatting of this question, ResearchGate is...
06 June 2018 10,070 3 View
I have a SAM file full of aligned reads. They will be made up for 5-to-3 prime and 3-to-5 prime. I am only interested in working on the 3-to-5 prime. How can I identify one from the other?
06 June 2018 7,170 0 View
I understand how survival methods can be used to determine the probability of survival given a dataset of 'time-to-events' with almost all examples considering cases of Alive/Dead e.g., cancer....
05 May 2018 1,388 3 View
I have a medical longitudinal retrospective dataset, records between the observation period of 2000 and end 2016. For many reasons not every medical record spans that entire time-frame, e.g. the...
05 May 2018 3,328 8 View
I am using Gromacs with the Amber FF family. I am able to calculate bonded force constants for post-translationally modified amino acids, but I am unsure of how to calculate the non-bonded LJ...
02 February 2018 7,113 2 View
I would like some thoughts on a way of quantifying a simple measure of lipid chain order parameter from a gromacs file. The g_order will give me an average and an error term for each of the...
02 February 2018 8,208 8 View
I would like to try, for my first time, modelling the interactions between protein and DNA in an aqueous environment using Molecular Dynamics. I have the latest Gromacs distribution available....
01 January 2018 4,956 4 View
This is my first ever medical statistics/epidemiology questions, so please be patient if I come across as naive, I normally focus on drug and protein chemistry. I have a huge medical dataset....
12 December 2017 8,802 6 View
I have two all atom molecule dynamics systems of a protein. One is a wildtype and the other is a mutant. They differ by amino acid sequences. I am running my simulations in Gromacs. Each system...
12 December 2017 9,356 5 View
I have a system on N peptides. They are tightly packed into the unit cell, so peptide A thinks peptide Z is its neighbour, due to PBCs. A bit like lipids in a bilayer. I would like to take the...
12 December 2017 6,213 3 View
Hi, I am having a hard time understanding the description in the manual with regards to periodicity. Is the manual referring to PERIODIC and NOPBC as two separate things or one and the same? I am...
12 December 2017 6,588 0 View
It's been many years since I last used PLUMED with gromacs and there bits that I have forgotten about and some new features etc., that I am a little unsure of. For now, I would just like to...
12 December 2017 3,011 3 View
I'm having some issues resolving artefacts generated during RMSF calculation of a protein from its crystallographic unit cell conditions. Using a combination of trjconv -pbc adjustments I'm able...
10 October 2017 4,344 6 View
I was wondering whether there have been any developments in protein insertion into computational lipid bilayers over the last two/three years? I am using Gromacs and the protein has over 8 TM...
07 July 2017 8,717 0 View
A rather basic question just to make sure I understand some of the theory. I have an amino acid backbone, with the amine and carboxyl groups positively and negatively charged, respectively...
05 May 2017 8,516 15 View
Quite a few years ago I wrote a matlab script that would load in a trajectory (in the Gromacs .gro format) and measure the angle, relative to the average bilayer plane, of a transmembrane helical...
03 March 2017 9,453 4 View
I imagine a lot of detail will be lost during the asking of this question, but I will try my best. I am using Gaussian to work through a reaction mechanism, roughly 15 steps. We believe the 10th...
03 March 2017 2,489 10 View
Hi all, I'm not actually asking for help, I'm more interested in opinions. I will usually perform all OPT reactant and product at a basis set of 3-21G (because they are very quick and my molecule...
03 March 2017 2,531 11 View
If you perform a restart on any Gaussian job it will write over the contents of the earlier .log/.out file. Typically, an incomplete log./.out file can be loaded in GView showing the results thus...
02 February 2017 1,270 4 View
Hi all, I am having great difficulty taking my Gromacs MARTINI coarse grain model of a protein to a dt of at least 0.025 fs. I have modelling my protein using the Martinize of an atomistic...
01 January 2017 8,068 3 View
Should the pressure and temperature coupling in Gromacs (tau_p and tau_t, respectively) reflect the size of the integration time step? For example, in a CG simulation you may have the .mdp...
01 January 2017 5,215 0 View
I have derived force constants for MD simulations from vibrational frequency calculations of QM Gaussian calculations. The QM to MD force constant conversion is from my own software. Now that...
01 January 2017 9,801 6 View
In QM software, such as Gaussian, it is very common to apply a scaling factor to frequency values. However, despite my best efforts, I am unable to find a credible source that explains why and I...
01 January 2017 9,237 7 View
A simple question, perhaps badly phrased in the title, what is the largest singular biomolecule i.e., not stacks of carbohydrates one after the other, to be involved in post-translation modified...
01 January 2017 566 3 View
I always think of a heme cofactor with bound iron as a flat molecule. However, after reparameterizing heme without iron for the purpose of an MD simulation, the cofactor demonstrates quite a...
09 September 2016 3,957 4 View
Hi all, I have successfully installed Gromacs on an F16 Ubuntu Virtual Machine on Azure using a Microsoft Sponsorship. I have executed, in real time from an SSH command line, the benchmark...
08 August 2016 3,581 0 View
With DFT (wb97xd/6-31+G(d,p)) using Gaussian I am having great difficulty optimising a pair of reactants in complex i.e., my organic (which is part of a glycated side chain of a protein) with an...
08 August 2016 9,796 16 View
I want a good measure for water content around a wild type side chain, and then a measure around the glycated form of that side chain i.e., a comparison of two individual systems. I think that...
07 July 2016 8,710 7 View
Out of interest, I would like to know who has reported and for what reason a set of quantitative results using the total energy of an MD study? That is, the total energy reported at the end of the...
07 July 2016 8,270 7 View
I have two setups for a cluster of rod shaped proteins as a surface with water on the outside (it is a fibril of collagen protein, periodically stacked in the x-y dimension and a long water box in...
05 May 2016 1,698 5 View
I am trying to remove an -OH group from a ring structure using DFT/ab initio after having closed a carbon ring structure (Re->TS1->Int1, below). -OH is extremely difficult to remove as it...
05 May 2016 4,110 15 View
Hi all, I am trying to find as many techniques for water hydrogen bond dynamics (i.e., solvent shells) around an organic molecule e.g., amino acid, of interest. The software package must be...
04 April 2016 3,532 5 View
I'm performing a bond scan using mod redundant in Gaussian. Unfortunately it is taken quite a long time and I have had to perform a restart. This has over written the .log/.out file, so it now...
04 April 2016 3,038 0 View
Using Gaussian to calculate DeltaG standard state (a change in Gibbs free energy), the Gaussian website have provided an example which results in a DeltaG>0 kcal/mol. This would suggest that...
03 March 2016 5,016 1 View
The Gaussian output (in GView and as part of the output) report two bonds as: 0.963 0.958 Is the final significant as reported by Gaussian and uncertain term? Should I report the bond length...
03 March 2016 6,645 9 View
In Gaussian, the Force Constant matrix (unweighted hessian) can be found in the formatted check point file. I would just like to double check a few things: 1) Are the hessian units...
02 February 2016 2,144 3 View
I have found a transition state: Frequencies -- -1250.5167 15.3797 20.7708 Which clearly shows a water mediated proton shift off a carbon, through the water, then...
01 January 2016 4,647 4 View
What is the very latest means using Gromacs for inserting a TM alpha helical dimer into a lipid bilayer? Also, what are the latest techniques for measuring lipid bilayer surface area with an...
01 January 2016 4,989 3 View
Unfortunately my capping groups (NME and ACE) which I had to put in myself for the Amber forcefield in Gromacs have a long bond each. It is just long enough to throw a LINCS error, yet, running an...
01 January 2016 578 0 View
I've only seen this warning reported twice, both times I don't think a solution was presented. I ran IRC in Gaussian over a TS found at wb97xd/3-21+g with no problems at all. But when I take the...
01 January 2016 1,102 0 View
Quite a basic QM quesiton: I have an isolated system (in vacuum). The nitrogen in the schiff base of my reactant will become protonated from a neighbouring water molecule. My product is thus a...
01 January 2016 6,662 10 View
I have an issue during QTS3 and TS searches. In a particular arrangement I am finding the last step reports: Maximum Force 0.013634 0.000450 NO RMS Force 0.003018...
01 January 2016 3,894 2 View
From an earlier question I was grateful to learn about the two step process for the movement of a double bond from a Schiff base (-N=C) down the backbone of a glucose molecule to form C=C. This...
01 January 2016 2,201 6 View
I have an alpha-helix embedded in a bilayer. I'm using gromacs 5+ and plumed 2.2. I want to encourage the protein to sample a 'rotation', so I can then put it up against another helix to find the...
11 November 2015 4,455 5 View
I'm using plumed 2.2 with Gromacs 5. I am currently struggling to cover a sufficient range of my three collective variables, two torsional (dihedral) and one distance. My system essentially...
11 November 2015 2,323 7 View
I've performed many umbrella sampling and meta-dynamics simulations to report the interaction energies (free energy of association, for example) of proteins. However, I am curious as to how useful...
11 November 2015 799 3 View
Hi all, Rather a simple request here. If I have a large molecule, say 55 to 70 atoms big, it is bound to have several energy minima. One example being, if this were a derivative of a sugar like...
11 November 2015 3,944 5 View
Do potential energy functions in MD forcefields have a sense of mathematical identity with their force constants between two atoms A and B? I am using an Amber Force Field (so that is...
10 October 2015 3,346 0 View
Hi all, I’m a little stuck on deriving an angular force constant for the amber forcefield. Consider in amber, that the potential energy from the angle ABC is: U_{ABC} = K(theta - theta_eq)^2 The...
10 October 2015 7,680 4 View
Hi all, I am trying to work out the angular force constant from the frequency calculation of an ab initio Hessian for a mechanical force field (amber). The force constant of bond stretching is...
10 October 2015 975 4 View
Using Gaussian I've found a TS using wb97xd/3-21+g (set to opt=tight). The Freq gives me a single imaginary number. I've very happy with this. Unfortunately, when I move it up to a wb97xd/6-31+g*...
10 October 2015 598 5 View
I have a frcmod.unknown after parameterising a structure using R.E.D. for an AMBER simulation. Thankfully all of the atom types are known (organic, no metals), however, the bond connectivity is...
09 September 2015 822 12 View
Hi all, I am trying to provide the force constants and distance/angles in frcmod.user for a SECOND (follow-up) submission to R.E.D server so I have a complete amber force field. Unfortunately I...
09 September 2015 9,175 3 View
I'm searching for the accurate nomenclature of an isolated system under study involving one water molecule intermolecularly associating through hydrogen bonds with a glucose molecule. Would such a...
08 August 2015 10,075 2 View
I have performed a 200 ns MD simulation (Gromacs - Amber forcefield) using PLUMED meta-dynamics with a distance based reaction coordinate of protein A entering protein B. I do see some noticeable...
08 August 2015 3,757 8 View
I am using the Amber force field in Gromacs on a compound that I do not have a topology for (I do NOT have a copy of AMBER itself). There are no metals, simply O, C, N and H (it is a derivative of...
08 August 2015 1,272 5 View
Is there a simple tool or 'how to' to derive force constants from Gaussian's vibrational frequency analysis? I understand from the G09 white paper when force constants are calculated (and the...
08 August 2015 9,033 7 View
Of 54 atoms in my structure (a solute and a water molecule) in an implicit solvent (water), using Gaussian 09, I performed a high level DFT geometry optimisation: wb97xd/6-311++g(2df,2p). Using...
08 August 2015 2,377 11 View
In Gaussian, the totally energy of my system has been reported using "Sum of electronic and zero-point energy" (output from the FREQ). This value though, hasn't been scaled to take into account...
07 July 2015 6,169 13 View
I am using flexible enforced rotation on a long narrow protein against the entrance to an enzyme active site. I am trying to rotate the narrow protein 360 degrees so I can then capture windows for...
07 July 2015 2,317 2 View
Hi all, I've noticed some functionals differ by as much as 2 kcal/mol in hydrogen bond disassociation when the relative total energy is corrected using the BSSE. Unfortunately, the literature I...
06 June 2015 8,142 7 View
I would like to convert a gaussian checkpoint file into a .wfn file for the use in multiwfn software. I understand .wfn can be generated at runtime using output=wfn, but I've only just learned...
05 May 2015 9,834 3 View
Hi all, I fail to see why a Forward IRC calculation fails when I used the results from a successful opt+freq calculation. The original opt+freq was: hf/3-21+g* opt=(tight,calcfc)...
05 May 2015 6,406 10 View
I have an organic molecule with N number of explicit water molecules presumably hydrogen bonding to the molecule's -OH group. Besides angle and distance criteria, is there anything quantitative...
05 May 2015 3,442 21 View
I have a compound, which we expect interacts with water. Experimentally the level of hydration in a tissue samples changes upon including this compound. We aren't exactly sure, though, how (if)...
03 March 2015 6,655 9 View
Hi all, I'm having trouble coming up with a design for a 'stable' dihedral measurement along the principle orientation of a helical protein in a GROMACS topology. I will use this measurement as a...
03 March 2015 1,528 1 View
I am struggling to complete the next step of a (in theory only) reaction pathway involving the closure of a 7-membered ring via a proton transfer to protonate a carbonyl which allows a...
03 March 2015 3,760 4 View
When you set up the initial geometry of a TS in Gaussian, should I be modelling the charge and spin multiplicity of the TS itself or either the product/reactant? For example, in the case of...
03 March 2015 5,653 5 View
I'm typically used to rendering large protein structure in VMD, however, I now have a small compound that's been optimized in GAUSSIAN and I wish to present the output as suitable as I can, i.e.,...
02 February 2015 3,168 8 View
Hi all, Until last night I've only ever had this one before. After two days of calculating opt=(ts,noeigentest) freq=noraman my system converges and then goes on to perform a frequency...
02 February 2015 6,678 7 View
Hi all, I have 3D data which I am trying to splot in GNUPLOT. The z-range of values is negative, going from 0 to -300. For some reason in both my X11 and postscript terminals the plane has been...
01 January 2015 3,345 1 View
Dear all, Using Gromacs, I'm able to record the number of hydrogen bonds between two proteins (no overlap) as a function of time. I am interested though in which particular pair of...
01 January 2015 2,618 3 View
Dear RG experts, I'm playing with Meta dynamics for the first time and I'm struggling to come up with a way of rotating my ligand in the catalytic site of an enzyme. The ligand is a long narrow...
12 December 2014 9,174 4 View
Hi all, I am trying to prepare a computational model of a particular protein (matrix metaloproteinaise 1 (MMP1)) found in the extracellular matrix of humans. However, I am struggling to find a...
12 December 2014 841 4 View
I’ve been asked to study using DFT (wb97xd/lanl2dz). Prior to introducing Cu(2+), my structure seems reasonable enough yet when Cu(2+) is introduced at a particular site, the C-C bond prior to the...
12 December 2014 4,828 4 View
I have two zinc coordinations in my globular protein, using Amberssff in Gromacs. Partial charges have been calculated for both using PyRED. One zinc remains in place using a non-bonded model,...
12 December 2014 8,127 2 View
Hi all, I have done this countless time and I've "googled" this a lot. Unfortunately I have a simulation that simply won't behave. I am trying to visualise (and analyse) a trajectory in VMD after...
11 November 2014 1,413 14 View
Hi all, I have successfully derived partial charges using RED for two separate zinc binding domains in a protein. All the settings were carefully selected for the Amber sb99 FF and the structure...
11 November 2014 5,329 1 View
Hi, I'm trying to extract the "valence" and "all" NBO from my gaussian 09 calculation using cubegen to then load into VMD. Unfortunately, if I supply MO=valence or MO=all, I get a floating point...
11 November 2014 1,492 1 View
Hi, I am trying to calculate partial charges for Zinc in the cat site of an enzyme. The crystal structure shows a zinc ion with a coordination of three HIS residues, with zinc held in place by the...
10 October 2014 8,663 8 View
Hi, my apologies if this is quite rudimentary, I am having to learn a lot whilst racing against the clock. I am trying to calculate the charge and spin multiplicity for Cu(+2) ion sitting between...
10 October 2014 1,889 6 View
Hi, In short I am getting a bit overwhelmed with the difference in nomenclature used by the Gaussian output, text books, and people's suggestions. I am trying to pin point the most energetically...
10 October 2014 7,844 7 View
Hi all, I've decided to try some bench marking with respects to performance and given that I have plenty of memory to play with I thought I would start by preserving all of the integrals using...
09 September 2014 2,654 1 View
Hi, This is going to be a tricky question to phrase given that I am not too familiar with the subject matter. I was discussing Gaussian results with one of the earlier developers last week. We...
09 September 2014 1,489 3 View
I am trying to speed up the discovery of a transition state. I know what the TS looks like, so I thought I would try and get the system to co-operate more by specifying what bonds should...
09 September 2014 8,165 5 View
I've found my transition state, and now I am performing an IRC calculation (forward and reverse, ten steps each way, twenty in total). I don't understand the final message at the end of the log...
09 September 2014 6,210 2 View
I have derived the partial charges for a zinc ion in a catalytic site of an enzyme using R.E.S.P for the Amberffsb force field. For two of the three transition metals (the third belong to the...
08 August 2014 7,018 5 View
I am using Gaussian, DFT (probably B3LYP or WB97XD). As an example, if I have an amino acid; any particular one as this is just an example of my compound, and I want to see how the structure and...
08 August 2014 9,549 9 View
I have successfully modelled the reaction pathway for the nucleophilic addition of an electronegative nitrogen attacking a slightly electropositive carbon. What was a double bond of an oxygen to...
07 July 2014 5,073 2 View
A bit of a layman question. If I have a reaction mechanism which I suspect has about 18 intermediate steps, is it wise to take each step one at a time? i.e., I optimise my reactant and product,...
06 June 2014 307 5 View
I am able to run both ab initio calculations and MD simulation. However, I am relatively new to parameterising non-bonded interactions (transition metal in an active site supported by non-bonded...
05 May 2014 4,928 2 View
I seem to be consistently producing link 9999 errors during a TS search of a structure I generated from a mod-redundant scan geometry. As an example, I scan geometry modifying the bond length...
05 May 2014 2,158 15 View
I have an enzyme and a protein ligand bound. In the active site of the enzyme is a ZN2+ ion. I am using the latest version of gromacs with the Amber99SBFF. After carefully settling my solvated...
05 May 2014 9,189 3 View
To my understanding the nucleophilic attack of H2C=O is a two step process: 1) The slight positive charge on the carbon is open to attack by a nucleophile. The C=O loses its pi bond and reduces...
05 May 2014 973 6 View
I have had success viewing the reaction coordinate of a bond scan in GView for a single input file. However, after having performed 6 restarts on a cluster with a 48 hr wall time I can't seem to...
04 April 2014 9,909 0 View
I'm having a go at calculating the free energy of solvation of two small proteins, as separate systems. I am using the Bennett Acceptance Ratio approach by coupling the coloumbic and van der Waals...
01 January 1970 5,888 10 View
I have a TS, the vibration of the negative frequency looks very promising. However, my first few efforts to perform an IRC have resulted in both forward and reverse directions producing *almost*...
01 January 1970 6,330 7 View
