[gmx-users] top file for two seperate peptides

[Qian Wang]

Hi,
 
It works. Thanks a lot.
 
Sincerely,
Qian

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Wednesday, October 13, 2010 2:28 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Gromacs Users' List <gmx-users at gromacs.org>

> 
> 
> 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
> 
> ========================================
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