[gmx-users] Doing restart

#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted {margin-left:0 !important;border-left:1px #715FFA solid !important;padding-left:1ex !important;background-color:white;} Dear gmx users I stoped my md simulation and now i want to restart it. I use gromacs 2016.3  and issued

Re: [gmx-users] ligand

Hi Justin Thank you so much with best Farial From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Monday, 14 August 2017, 16:35:58 Subject: Re: [gmx-users] ligand On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote: > Dear Justin > Thanks for your adv

[gmx-users] ligand

Dear GROMACS users I noticed my ligand has some broken bonds and changes in atoms arrengement after md simulation was done. I have read before that no bond is broken and created in simulation . So why have been ligand changed ? I think, i have to notice that when i wanted to create a ligand

Re: [gmx-users] ligand

Dear Justin Thanks for your advice.Now I am trying to create a .gro file from the united atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o xxx.gro but faced to this warning: WARNING: all CONECT records are ignored would you please advice me how can i solve this problem?

[gmx-users] Equilibration

Hi Justin Thank you so much for your reply about minimize ligand in vacuoaccording to :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I minimized my protein and ligand alone to fix the problem (  LINCS warning, ( one or more water molecules can not to

[gmx-users] ligan minimization in vacuo

Dear gmx-users I have a problem in equilibration my protein-ligand complex and encountered to this error after 2 steps of 5 steps:one or more water molecules can not be settled. check for bad contacts or reduce the time steps. so I decided to create a topology for my designed drug (50

[gmx-users] how to creat ligand topology to minimize in vacuo in the absence of the protein

Dear gmx-usersI need to create a topology for my designed drug as a ligand to minimize it in the vacuo in the absence of the protein. But I dont know how can i convert the DRG.itp file which I obtained from PRODRG site to a .top file . I searched in the Google and found " Re: minimizing ligand

[gmx-users] equilibration

Hi justin  Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and

[gmx-users] pdb2gmx

Hello  I want to create a .gro and .top file from my protein that contains 379 aminoacids in it's .pdb file by using gromos96 54a7 force field: pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and topology files are created , I see that message: Start terminus GLY-12: GLY-NH3+

[gmx-users] ATB and PRODRG

Dear gmx users I am using gromos96 54 a7 and gromos 96 a1 force fiels to simulate tow various complexes  ( protein + ligand). and  used ATB and PRODRG  to create topology files for them, respectively. I dont know anything about editing ATB and PRODRG' topology files but reassigingn their

[gmx-users] EQUILIBRATION

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but when I wanted to performance equilibration , i got this ERROR: step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if

[gmx-users] remove the jumps over the boundaries

Dear GROMACS users I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD , it has pbc problem, so I issued this command: trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10 but

Re: [gmx-users] peptide ligand

Dear Justin I performed NVT equilibration for 300 ps , it was done successfully. Yesterday I wanna do NPT equilibration , so used your npt.mdp file in the GROMACS tutorial and replaced energgroups and tc-groups by Protein and Protein water-ions, respectively, specified nstep = 15 , but when

Re: [gmx-users] peptide ligand

Dear Justin Thank you so much for all of your help best Farial From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Wednesday, 4 October 2017, 15:19:38 Subject: Re: [gmx-users] peptide ligand On 10/3/17 1:51 PM, farial tavakoli wrote: >  blockquote,

[gmx-users] peptide ligand-protein complex topology

Dear GMX users I want to generate a topology for my peptide ligand, but I dont know if I can use "gmx pdb2gmx -f peptide ligand-protein complex.pdb -o peptide ligand-protein complex.gro -water spce -ignh" ?would you please advice me that how can I generate a peptide ligand topology file? I

[gmx-users] peptide ligand

Dear GROMACS users I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B) and converted it to .itp file to string it in Protein.top file, then, added Protein_chain_B in [ molecules ]