[gmx-users] top file for two seperate peptides

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 12 20:07:25 CEST 2010

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.


> 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


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