Percentage of potential SASA of ligands in Gromacs??

Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance.

03 April 2019 6,200 2 View

How to generate the wfn file in gaussian ?

Hi all, I have gauss view (6.0.16) and gaussian16W for microsoft windows. I want to generate the wfn file. I have tried specifying of C:\path\molecule.wfn in molecular specification section...

11 December 2018 7,311 0 View

How to guess time taken to complete a QM/MM job in gaussian ?

Hello everyone, I have run optimization of protein-ligand complex using QM/MM in gaussian. I did not find any criteria to find how much time will be taken to complete this job. Is there any...

10 November 2018 9,208 0 View

Suggestion for combing of processors on server??

Hi everyone, We have HP server consist of 160 processors on 80 cores (i.e. each core has 2 processors). We want to utilize this server for molecular dynamics work. So we want to combine like 60...

02 March 2018 2,608 0 View

Error in generation of frcmod of FES in AMBER ?

Hi everyone, I have to do Molecular Dynamics Simulations of a FE2S2 center containing protein. I need to generate the FE2S2.mol2 and FE2S2.frcmod files. I have used the antechamber and parmchk...

11 December 2017 1,826 0 View

Query about FES cluster topology in GROMACS?

Hi everyone, I have run the molecular dynamics of FES cluster containing protein in GROMACS. I got the error that FE and FES are not found in the amino acid database of force field. What can i...

10 November 2017 9,793 0 View

Occupancy of hydrogen bonding in VMD after molecular dynamics ?

Hi everyone, I have done molecular dynamics simulation of protein with ligand in GROMACS. I am not much aware of occupancy of hydrogen bonds in complexes. What does occupancy of hydrogen bonds...

09 October 2017 2,652 0 View

Hydrogen bonding distribution in molecular dynamics simulation in gromacs?

08 September 2017 852 0 View

Error in MD by gromacs

06 July 2017 8,975 0 View

Consideration of one chain or two chains in MD by Gromacs

Hi all, I have to do molecular dynamics of a protein. it is trimer of dimer. It has total 6 chains Although in dimer both chains have same amino acids. It has 6 ligands. Ligand interact via...

06 July 2017 6,005 6 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Energy minimization in LAMMPS using NVT ?

How do I do energy minimization in lammps with NVT ensemble ? I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search...

01 March 2021 2,294 3 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View

Why the CHi^2 is close to zero with a bad fitting but the Rp and Rwp are still high?

I am refining my XRD data using in FullProf program. The intensity of the modulated X-ray peaks is almost flat. I tried to adjust the peak intensities but unsuccessful. What is the reason? I guess...

23 February 2021 2,304 4 View

Can we use a compensation matrix with single staining that the negative population for each single staining is below zero?

Recently we used single staining to make a compensation matrix. But, for each single staining we saw that 13 to 25 percent of our negative population had been shown below Zero. In this situation...

21 February 2021 9,982 2 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How to compare means of continuous data with zero-inflation and skew?

I have two groups (unpaired) of plant biomass measurements and want to know whether there is a test that can be used to determine statistical significance where assumptions are not violated. The...

18 February 2021 1,258 4 View

Will SARS-CoV-2 Spike be broken into S1 and S2 by denaturing conditions?

Hello, I am performing a western blot of my SARS-CoV-2 Spike-pseudotyped lentiviral particles. I denature my virus by adding concentrated virus to 2X Laemmli buffer at 1:1, then boiling for...

17 February 2021 4,844 4 View