Qian Wang wrote:
Hi,
Thanks. Now I add TER after every peptide coordinates. But then when I
used the command pdb2gmx -chainsep, it said "invalid command line
argument: -chainsep". So I am wondering the version I use is different
or something. My version is gromacs 4.0.7.
The -chainsep option was introduced in version 4.5. With older versions I think
you should just be able to use -ter to interactively assign the protonation
state of the termini.
-Justin
Sincerely,
Qian
----- Original Message -----
From: "Justin A. Lemkul" <[email protected]>
Date: Wednesday, October 13, 2010 2:08 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Discussion list for GROMACS users <[email protected]>
>
>
> Qian Wang wrote:
> >Hi,
> > I want to simulate two seperate peptids in one box. However,
> when I use pdb2gmx to build the top file of this system, I found
> that gromacs thought there is only one peptide because it added
> bond, angle and other energy terms between the termius of these
> two peptides. Is there any way to prevent this problem, or I
> need to change the top file by hand? Thanks a lot.
>
> When pdb2gmx processes an input coordinate file, it will assume
> the amino acid sequence is one continuous protein unless you
> have either TER delimiters between the chains or the chain ID
> (A, B, C...) changes. Then apply the appropriate option to
> pdb2gmx -chainsep.
>
> -Justin
>
> > Sincerely,
> >Qian
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
MILES-IGERT Trainee
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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