[gmx-users] Re Multiple Chains

C Johnson helstreak at hotmail.com
Thu Sep 16 04:02:58 CEST 2010

genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro

Have you done any basic tutorial material before diving head-first into this 
more complicated topic?

The idea is this: pdb2gmx generates the topology for the protein.  You can then 
do whatever you choose with this definition of a protein.  After pdb2gmx, you 
also have a coordinate file that meets force field specifications as far as 
protonation goes.  This is the set of coordinates you should replicate, since it 
is correct within the force field.

I've done all the tutorial material hat is supplied with Gromacs...

I believe I may have got it.  These are the steps I took.

pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro

vi polygly.top
Changed Protein count from 1 to 8

genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro

editconf -f polygly_8 -o -d 1.0

genbox -cp out -cs -p polygly -o b4em

grompp -v -f em -c b4em -o em -p polygly

mdrun -v -s em -o em -c after_em -g emlog

grompp -f pr -o pr -c after_em -r after_em -p polygly

mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &

grompp -v -f full -o full -c after_pr -p polygly

mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &

When I look at the simulation:

ngmx -s pr -full

There are 8 short peptides.

Does anything seem wrong with these steps?

Justin, thanks for the help :)

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