Hassan Aryapour

6 Questions 8 Answers 0 Followers

Questions related from Hassan Aryapour

Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

I would like to calculate the presence of water molecules number as a function of time, around a ligand during binding to its pocket from a trj.xtc file. How can I do it by Gromacs or any other...

11 November 2018 9,274 10 View

Getting an fatal error when rerunning .trr trajectory in Gromacs?

Dear Gromacs Users When I rerun .trr trajectory files for re-calculating energies and forces, the following error was received. Any suggestion to solve it please? However, there is no problem with...

07 July 2018 9,853 1 View

How to calculate the oxidation number of Fe atom and the multiplicity of a Fe2S2 cluster?

I want to calculate Fe2S2 charges in a protein complex, but I don't know how to obtain the multiplicity, suitable oxidation number of Fe in Fe2S2 cluster, Is it oxidation state +3 for Fe? Which...

12 December 2016 6,333 4 View

Is there a program to create topology files (.rtp, .itp, .hdp .atp and .dat) for various force fields in gromacs from a New Residue PDB file?

Dear Researchers I have already used from gromacs manual for editing topology files (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), but I am looking for program...

09 September 2016 622 9 View

How to resolve "make check" tests errors in gromacs installation?

Dear Gromacs UsersI want to install gromacs 5.1.2 in my laptop, when I used "make check -j 8" command, the following errors was appeard, MdrunTests (19) and MdrunMpiTests (20) were failed, How can...

06 June 2016 6,465 2 View

How can I make a movie from gromacs trajectory file (200 ns)?

VMD failed because of low memory of computer (16GB) for resolving this problem, Can I split .xtc files to two parts? How?

11 November 2015 6,325 8 View