Fwd: [gmx-users] scripts to generate topology CG

[Francesco Pietra]

---------- Forwarded message ----------
From: Francesco Pietra <francesco.pietra at accademialucchese.it>
Date: Fri, Oct 23, 2009 at 5:01 PM
Subject: Re: [gmx-users] scripts to generate topology CG
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>


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?

I forgot to add that the graphic program uses the above grep command,
giving the same number of W as the line command. The number of DCCP is
diminished by those deleted in inserting the protein, but the grompp
command complains that .gro does not matches .top. If no further water
is added graphically, everything works.

>
> -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.

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
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>