[gmx-users] Multiple Chains

[Justin A. Lemkul]

C Johnson wrote:
> Hello all,
> 
> I attempted to use a single pdb file with a single peptide 
> chain  (speptide.pdb from the tutorial) for a multiple chain 
> simulation.  This is what I did:
> 
> pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
> 
> I then used vim to edit the section:
> 
> [ molecules ]
> Protein            1
> 
> changing Protein from 1 to 2.
> 
> then I did the following commands:
> 
> editconf -f speptide -o -d 0.5
> genbox -cp out -cs -p speptide -o b4em
> 
> They seemed to work fine, it was when I used grompp that I received error:
> 
> grompp -v -f em -c b4em -o em -p speptide
> 
> Fatal error:
> number of coordinates in coordinate file (b4em.gro, 2741)
>              does not match topology (speptide.top, 2932)
> 
> What have I done wrong?
> 

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.

-Justin

> Thanks for your help,
> Casey
> 

-- 
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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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