[gmx-users] peptide ligand

[Justin Lemkul]

On 10/3/17 1:08 PM, 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; }  So how should I split protein and ligand from each other to create  .mdp files?
> 

I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index files 
and now .mdp files? I'm lost, and it's very hard to provide help.

If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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

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