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
a
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 o
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 atoms)
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 b
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 issu
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+
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 charges
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 f
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 top
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?
Hi Justin
Thank you so much
with best
Farial
From: Justin Lemkul
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 advice.Now I am trying to cr
#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
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 think
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 ] directive
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, div.yahoo_quoted { margin-left
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
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