[gmx-users] scripts to generate topology CG

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 23 16:14:37 CEST 2009



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

> 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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