system in the corner as you described.
Using editconf should eliminate this problem.
-Justin
francesco
-- Forwarded message --
From: Francesco Pietra
Date: Sun, Oct 25, 2009 at 6:22 PM
Subject: Re: Fwd: [gmx-users] scripts to generate topology CG
To: jalem...@vt.edu, Discussion
, 2009 at 6:22 PM
Subject: Re: Fwd: [gmx-users] scripts to generate topology CG
To: jalem...@vt.edu, Discussion list for GROMACS users
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote:
>
>
> Francesco Pietra wrote:
>
>>> grep W solvated.gro | wc -l
>>>
Francesco Pietra wrote:
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote:
Francesco Pietra wrote:
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,
I don't understand this statement.
giving the
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote:
>
>
> Francesco Pietra wrote:
>
>>> 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,
>
> I don't understand this statement.
>
>> giving the s
Francesco Pietra wrote:
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,
I don't understand this statement.
giving the same number of W as the line command. The number of DCCP is
diminished by those de
Francesco Pietra wrote:
On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul 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
-- Forwarded message --
From: Francesco Pietra
Date: Fri, Oct 23, 2009 at 5:01 PM
Subject: Re: [gmx-users] scripts to generate topology CG
To: jalem...@vt.edu, Discussion list for GROMACS users
On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote:
>
>
> Frances
On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul 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 gra
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 someth
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
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
wrote:
> Hi:
> I am looking for scripts that generate topology in coarse grained.
> Thanks for indications.
>
> francesco pietra
> _
Hi:
I am looking for scripts that generate topology in coarse grained.
Thanks for indications.
francesco pietra
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