Re: [gmx-users] Modified peptides

Thank you very much Dr. Lemkul Sent from my iPhone > On 02-Apr-2016, at 10:34 pm, Justin Lemkul wrote: > > > >> On 4/2/16 2:11 AM, sun wrote: >> Hello Gromacs Users I have already posted this query but in the absence of >> any suggestion, I am posting it again. I hope

Re: [gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

Yes sir, even though its not working On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul wrote: > > > On 4/17/16 11:35 AM, REMYA R wrote: > >> Dear sir, >> >> I am getting error while running simulation of Protein-Ligand complex , >> usong GROMOS force field, spc water model at

Re: [gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

On 4/17/16 11:35 AM, REMYA R wrote: Dear sir, I am getting error while running simulation of Protein-Ligand complex , usong GROMOS force field, spc water model at the equilibration phase of bevan lab tutorial for protein-ligand simulation, version 4.6.1 (

Re: [gmx-users] error in pdb2gmx

On 4/17/16 12:05 AM, Shahla Omidi wrote: ​hello I want to simulate my protein with charmm36, and I used gromacs505 for this I took this error with pdb2gmx "Residue 1 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction

Re: [gmx-users] Protein-ligand contact maps

On 4/17/16 3:58 AM, Patricia Jones wrote: Hello Dear Users I am using Gromacs 5.0 for protein-ligand simulation. After completing 50 ns MD following Justin's tutorial, I have used gmx_mdmat for protein residue contact matrix. Now, I want to use this command for protein-ligand atom contacts.

[gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

Dear sir, I am getting error while running simulation of Protein-Ligand complex , usong GROMOS force field, spc water model at the equilibration phase of bevan lab tutorial for protein-ligand simulation, version 4.6.1 (

[gmx-users] Protein-ligand contact maps

Hello Dear Users I am using Gromacs 5.0 for protein-ligand simulation. After completing 50 ns MD following Justin's tutorial, I have used gmx_mdmat for protein residue contact matrix. Now, I want to use this command for protein-ligand atom contacts. Is this possible using mdmat? or is there any