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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
