[gmx-users] Multiple Chains

C Johnson helstreak at hotmail.com
Wed Sep 15 21:42:49 CEST 2010

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?

Thanks for your help,

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