[gmx-users] scripts to generate topology CG

[Francesco Pietra]

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.

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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