[gmx-users] top file for two seperate peptides

Qian Wang 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:
> >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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101013/9b2e9088/attachment.html>

More information about the gromacs.org_gmx-users mailing list