17 Questions 17 Answers 0 Followers
Questions related from Vikram Dalal
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.
04 April 2019 6,289 2 View
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...
12 December 2018 7,440 0 View
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...
11 November 2018 9,266 0 View
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...
03 March 2018 2,674 0 View
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...
12 December 2017 1,911 0 View
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...
11 November 2017 9,862 0 View
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...
10 October 2017 2,737 0 View
Hi, I have run the MD of a protein by using Gromacs. I have generate the number of hydrogen bonds between protein and ligand by following command:- gmx hbond -f md_0_1.xtc -s md_0_1.tpr -num...
09 September 2017 937 0 View
Hi everyone, I have run molecular dynamics of a protein for 10 ns by gromacs 5.1.4. Due to power failure, my system shutdown just before 5 minute completion of my job. How can I resume my md run...
07 July 2017 3,997 2 View
Hi, I have tried MD of homology modelled protein by Gromos43a1 force field. After selecting the force field i got the error:- Atom HD1 in residue HIS 163 was not found in rtp entry HSE with 17...
07 July 2017 6,724 0 View
Hi everyone, I have modellled a protein by phyre. I got the 5 residues in outlier, so I tried modloop to build loop. When I used this model in gromacs for MD by CHARMM37. I got this error:- Atom...
07 July 2017 9,046 0 View
Hi everyone, I have to do molecular dynamics simulation of a zinc containing protein. I have kept the Zn molecule along with the protein and generate the topology file by using CHARMM36 force...
07 July 2017 7,403 0 View
Hi everyone, I have to do Molecular dynamics of zn binding protein by gromacs5.1.4. I found that i can use the CHARMM27 force field. But I am not able to get the tutorial for CHARMM27 for gromacs...
07 July 2017 1,082 10 View
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...
07 July 2017 6,073 6 View
I want to know that whether Kollman charges always positive or may be negative? Whether a protein may have zero kollman charge?
03 March 2017 1,662 0 View
I want to know that whether we can find solubility of a protein by computational tools??
03 March 2017 5,463 0 View
Hi everyone, I have to dock DNA with a ligand (cordinated with Mn and Cl). I can use autodock for it? If yes, is there any difference in protocol protein docking and DNA docking in autodock? If...
02 February 2017 3,039 6 View
