[gmx-users] peptide ligand

[Justin Lemkul]

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 <jalemkul at 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 <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

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