[gmx-users] Re Multiple Chains

Dallas Warren Dallas.Warren at monash.edu
Thu Sep 16 04:05:32 CEST 2010

Note that the genbox box stacking you are using here is not necessarily
what you want.  What sort of starting configuration do you want?  Is the
concentration / spacing that you get when you stack boxes like that,
actually what you want?  Or do you want a more concentrated type of
system where the molecules are intertwined etc.?


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of C Johnson
Sent: Thursday, 16 September 2010 11:57 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re Multiple Chains


genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro
Have you done any basic tutorial material before diving head-first into
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
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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