82 Questions 135 Answers 0 Followers
Questions related from Anthony Nash
I would appreciate people's thoughts on a methodology consideration. We're docking several thousand small molecules at a specific location on the receptor. We're using Autodoc Vina to reduce the...
01 May 2023 5,620 3 View
I've downloaded a text file full of curl and wget (two separate files) commands to download PDBQT files from ZINC20. However, none of the commands work. I've tried it on two machines using...
14 April 2023 228 1 View
Hi all, I am hoping for some assistance. I (the researcher) would like to know whether it is possible and how to go about building a Jupyter Notebook that a collaborator could load in their web...
27 January 2021 1,256 1 View
I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...
21 December 2020 7,958 2 View
Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...
18 December 2020 4,564 2 View
Hi all, Please imagine this to be a brand new machine with the latest installation of: Autodock Vina Autodock AutodockTools (MGLTools). I'm following a Nature Protocol for the prediction of...
15 December 2020 2,475 3 View
Hi all, I guess there are probably several ways of doing this. I'm looking to get access to every Pubchem CID. All compounds are published for download, but the files are quite large in size and...
02 November 2020 8,883 3 View
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...
11 January 2020 7,625 6 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...
14 November 2019 5,817 10 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...
31 August 2019 4,136 2 View
CMAP is a wealth of data, but I'm finding the sheer volume of transcriptional signature data generated given a drug (e.g., /sig amitriptyline) very hard to work with. The CLUE website will use...
03 July 2019 272 0 View
I am performing a PWP (conditional) recurrent cox regression analysis over medical records. For each individual, events are indicated by dates in their medical record. It is, therefore very easy...
19 December 2018 9,936 0 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...
05 October 2018 2,619 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...
23 September 2018 4,892 3 View
I am after some suggestions on what statistical analysis I can perform to show a before-and-after effect in a longitudinal electronic healthcare record (EHR). I have N number of EHRs, of varying...
14 August 2018 5,228 2 View
Hi, this is quite a basic question I feel, but I'm not exactly sure of what the best practice would be. I am currently using IGV for an interactive view, but I would rather have this automated on...
21 June 2018 7,374 2 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...
31 May 2018 6,195 7 View
I am performing a literature survey and I am looking for as many computational chemistry studies of Advanced Glycation End-products (AGE) as possible. I am interested in any and all AGEs...
14 April 2018 9,243 2 View
Consider a scenario where I have gone from a SMILES to a 3D structure (using openbabel). I then perform anyone of the openbabel finger print algorithms on that 3D structure before and after I run...
22 March 2018 8,757 3 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...
04 February 2018 5,972 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....
27 January 2018 8,509 2 View
Does anyone have a reference to a chemical structure of a lipid after it has undergone a non-enzymatic glycation event with glucose (or any other sugar)? Proteins can undergo non-enzymatic...
10 January 2018 9,421 4 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...
27 December 2017 4,177 4 View
Before science, I was a software engineer. But back in 2002-2006 I was building Java 2EE servlet driven webpages on an Apache Tomcat Webserver, communicating with a Microsoft SQL Server Manager...
20 May 2017 4,337 5 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...
18 May 2017 8,217 14 View
I've asked this several times now, and it is a step in a very long (16-20 steps) reaction mechanism that takes anywhere between 1 to 2 months to produce the end product. Imagine halfway through...
11 May 2017 5,537 1 View
A total open question. How would one go about linking a function to a protein given only its structure? I understand this is a million-dollar question, so vagueness is appreciated. I have a...
20 April 2017 925 5 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...
17 February 2017 4,086 3 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...
22 January 2017 6,243 5 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...
20 January 2017 3,566 3 View
Hi all, I'm quite new to homology modeling so I would appreciate some help. I'm yielding complete different search results when I submit an identical sequence with the same initial parameters to...
15 January 2017 2,936 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...
30 September 2016 5,707 3 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...
29 July 2016 1,568 6 View
What is the latest in free/open software to predict small molecule/ligand binding to proteins? I am running a Mac for GUI and a cluster of unix machines for computational calculations. A very...
27 July 2016 1,290 6 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...
23 July 2016 465 6 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...
29 May 2016 5,805 4 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...
04 May 2016 7,680 13 View
I have a very long pathway to map using DFT. There are approximately 15 intermediates. I am using Gaussian to capture the reactants, intermediates, transitions states and the products. I have so...
28 January 2016 8,971 3 View
Hi, I am struggling understand a mechanism, part of the amadori product rearrangement just after a Schiff base. As can be seen in the attachment, using DFT I'm trying to optimise both reactants...
31 December 2015 3,920 3 View
I am modelling a nucleophilic addition of an amine onto the carbonyl group of an organic. This eventually results in an immine (schiff base) after the deprotonation of the bound amine and the...
24 December 2015 2,289 4 View
Using Gaussian - DFT, wb97xd/6-31+g* default water solvent - I am really struggling finding the TS from an unstable carbinoamine (R-HC(OH)NH-R) to a schiff base (R-N=CHR). I believe there are two...
23 December 2015 6,477 4 View
Hi all, For a while now I have been building a small application to generate AMBER forcefield compatible force constants (stretch and angle). I use the full Force Constant matrix for a Gaussian...
22 November 2015 7,328 15 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...
20 November 2015 4,676 4 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...
15 November 2015 3,102 6 View
This hadn't really occurred to me until an experimentalist with no experience in computational chemistry asked me "to how many significant figures is Gaussian accurate when measuring distance?" I...
29 October 2015 8,159 5 View
I am reconstructing the force constants from the weighted hessian matrix, as calculated using HF/6-311+G(2d,2p) in Gaussian G09. The mathematics simple used a submatrix of the atoms of interest...
26 October 2015 910 7 View
I have written a short program which calculates the force constant of bond stretching and bond angle using a weighted cartesian coordinate hessian matrix from the output of Gaussian (opt and...
19 October 2015 8,264 11 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...
06 October 2015 1,209 3 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...
05 October 2015 1,012 3 View
How do I extract the whole Hessian from my chk/output/fchk Gaussian file? Note: The data in the .out file from a FREQ run is displacement and frequencies, NOT hessian data. The only think I can...
28 September 2015 5,026 18 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...
26 September 2015 9,823 11 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...
24 September 2015 3,291 3 View
This seems like it should be pretty obvious, but I have missed it completely! What are the units for the height and width (sigma) of the gaussian bias potentials used during a METAD (metadynamics)...
05 August 2015 5,679 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...
01 August 2015 4,571 7 View
Thrown into the deep end of Quantum Chemistry, I've finally made my way to CBS e.g., CBS-4M/QB3 etc... Under what circumstances would it be appropriate to use CBS in combination with a...
31 July 2015 6,621 1 View
Hi all, I find the use of the word 'restart' with respect to the Gaussian documentation to be a little vague. I have performed an IRC calculation (reverse) for 20 steps without reaching a minimum...
26 July 2015 1,987 2 View
Hi all, I understand this will have been covered before, but unfortunately efforts made by myself using the instructions in the PLUMED manual were not satisfactory. How should one go about...
18 June 2015 5,302 2 View
Hi all, I have some brilliant data with regards to hydrogen bonding between an organic molecule and explicit water solvents. The delocalised donor-acceptor occupancy levels and energies are all in...
23 May 2015 5,301 6 View
Hi all, Typically, restricted to electron structure of organic molecules and Molecular Dynamics, I've only just started to look into transition metal complexes. My question, to accurately model an...
16 April 2015 396 4 View
Hi all, I have a compound with a particular functional group surrounded by water molecules. I am using Gaussian G09 to optimise, first with HF/6-31+g** and then I will progressively move higher...
24 March 2015 664 12 View
Hi all, I'm considering running a handful of explicitly solvated (water) organic compound ab initio calculations in the presence of either a copper or zinc ion. I hope to find whether my compound...
17 March 2015 7,392 4 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...
04 March 2015 4,596 1 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...
02 March 2015 8,618 4 View
I have been approached by a colleague who is having difficulty executing OPT->FREQ->Pop(NBOs) over a number of structures. So I performed the OPT and FREQ separate from the population...
25 February 2015 348 8 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...
10 January 2015 7,195 1 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...
20 December 2014 4,941 3 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...
09 December 2014 3,307 6 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...
28 November 2014 8,631 1 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 6,518 19 View
Hi, I have a peptide fragment with a Cu^2+/Ag^+ accompanying ion. I want to optimise their geometry before I derive partial charges. I thought I would try a couple of different approaches. The...
26 October 2014 5,349 10 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...
19 September 2014 1,704 1 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...
22 August 2014 4,542 5 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...
06 July 2014 1,413 2 View
That is to say, as an atom is being displaced 0.1 angstrom from group A to group B (disassociation of a hydrogen, lets say), rather than saving each step from the Scan run as a separate opt=ts...
27 May 2014 8,499 1 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...
17 May 2014 6,502 2 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...
17 May 2014 2,209 3 View
I'm fairly new to the field of cheminformatics so I would be very grateful for experienced suggestions. I have three question (at the bottom), followed by two further questions that I thought of...
01 January 1970 304 3 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 2,720 9 View
Dear all, I'm hoping for a little bit of guidance. I'm using RDKit and sklearn to implement a random forest model trained using our drug screening (1600 drugs) results to predict new drug...
01 January 1970 9,142 2 View
01 January 1970 2,185 1 View
I am using various QM comp chemical techniques in an effort to capture the transition state between a protonated nitrogen and a hydroxyl group. I am struggling to find a stable product when the...
01 January 1970 148 3 View
01 January 1970 3,696 0 View
