[gmx-users] peptide ligand

[Justin Lemkul]

On 10/3/17 9:17 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
>
> Thank you so much for your reply.
> You mean , I should generate a topology file for my complex instead of 
> creating topology for each of them separately ?
>

As long as the protein and peptide ligand are denoted as being in 
separate chains (different chain ID or use of TER in the PDB file), then 
pdb2gmx will do everything for you.

-Justin

>
>
> ------------------------------------------------------------------------
> *From:* Justin Lemkul <jalemkul at vt.edu>
> *To:* gmx-users at gromacs.org; ‪farial tavakoli‬ ‪ 
> <farial.tavakoli at ymail.com>
> *Sent:* Tuesday, 3 October 2017, 16:35:49
> *Subject:* Re: [gmx-users] peptide ligand
>
>
>
> On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
> > 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 to create one topology file for my complex. Created newbox 
> and solvate.
>
> You shouldn't have to do any topology manipulation. pdb2gmx handles 
> multiple
> chains natively without any additional effort on your part.
>
> -Justin
>
>
> > But when I gave this command:gmx grompp -f em_real.mdp -c 
> solv_ions.gro -p topol.top -o em.tpr
> >
> > I faced to this error:
> >
> > Group Protein_chain_B referenced in the .mdb file was not found in 
> the index file. Group names must match either [moleculetype] names or 
> custom index group names, in which case you must supply an index file 
> to the '-n' option
> > of grompp.
> >
> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is 
> Protein_chain_B , but GROMACS gives error.
> > Would you please advice me how can I solve this problem?
> >
> > Best
> > Farial
>
> >
> >
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
>
> ==================================================
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================