On 10/3/17 11:13 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Thanks alot for your advxe
I would really appreciate if you advice me more to split protein and ligand in
index file, I saw the index help , but couldnt find out how should I use “
‘splitch’ nr “ script to split them.
With best regardsFarial
Index files aren't used with pdb2gmx. The splitting functions of make_ndx break
a chain down into its component residues. That's not at all what you want to do.
-Justin
Sent from Yahoo Mail for iPhone
On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
