[gmx-users] top file for two seperate peptides
qwang at mail.uh.edu
Tue Oct 12 20:19:46 CEST 2010
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.
----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Wednesday, October 13, 2010 2:08 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Qian Wang wrote:
> > 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.
> > Sincerely,
> 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
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