[gmx-users] top file for two seperate peptides

[Justin A. Lemkul]

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" <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
>  > 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

========================================