[gmx-users] scripts to generate topology CG

[Justin A. Lemkul]

Francesco Pietra wrote:
> On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Francesco Pietra wrote:
>>> Hello Sunny:
>>> I had already generated a valid .itp file for my protein using
>>> seq2itp. That .itp works for both the protein itself and the protein
>>> graphically inserted into a bilayer. When I add graphically further
>>> water it does not work any more. I thought there is something else
>>> that manages water without putting it everywhere. That script does not
>>> help.
>>>
>> In order to get a solution to your problem, I think you're going to have to
>> explain your methodology more clearly, including command lines and actual
>> error messages.  How are you adding water "graphically"?  Is genbox not
>> working?  Can you not simply grep for the number of water molecules, i.e.:
>>
>> grep W solvated.gro | wc -l
>>
>> and use that number in the topology?
>>
>> -Justin
> 
> I'll organize to explain in more details. The methodology (all-atoms)
> is explained in a few papers of mine and supplementary material, for
> example: F. Pietra “ Docking and MD simulations of the interaction of
> the tarantula peptide psalmotoxin‑1 with ASIC1a channels using  a
> homology model” J. Chem. Inf. Model. 2009, 49, 972-977.
> 

I read the methods there, and one of your own references therein, but it doesn't 
really help that much.  I understand what you're aiming for, but atomistic 
system preparation in AMBER and coarse-grain system preparation in GROMACS is 
like comparing apples and oranges.  Seeing details of successful methodology 
doesn't illuminate the problems you're currently having.  I still don't know 
what you're trying to do in GROMACS that's causing a problem.

Again, it would be helpful to see the commands you're issuing, and any other 
pertinent information (especially error messages, topology snippets, etc) to 
better diagnose your problem.  If solvation is the issue, I maintain that genbox 
can do the job much like Leap does in AMBER.  You may have to take a few tips 
from this page about adding water:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

-Justin

> thanks
> francesco
> 
> 
> 
>>> thanks
>>> francesco
>>>
>>> On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra <mishra.sunny at gmail.com>
>>> wrote:
>>>> There is a seq2itp.pl script provided by martini folks in their
>>>> website. You can get it from there.
>>>>
>>>> Sunny
>>>>
>>>> On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra
>>>> <francesco.pietra at accademialucchese.it> wrote:
>>>>> Hi:
>>>>> I am looking for scripts that generate topology in coarse grained.
>>>>> Thanks for indications.
>>>>>
>>>>> francesco pietra
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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