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 <jalem...@vt.edu>
*To:* gmx-us...@gromacs.org; farial tavakoli
<farial.tavak...@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
jalem...@vt.edu <mailto:jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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