[gmx-users] Re Multiple Chains

[Justin A. Lemkul]

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

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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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