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,
Casey
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