[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 15 22:12:22 CEST 2010

C Johnson wrote:
>> You've indicated in the topology that there are two peptides, but you've only 
>> built a coordinate file that contains one.  If you want to simulate two 
>> peptides, you have to build a configuration that contains two peptides.
> Are you saying that I cannot use the pdb file with a single molecule?  I would have to make a pdb file
> with multiple molecules instead?

Precisely.  A topology file cannot modify a coordinate file, and vice versa. 
They are complementary.



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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