[gmx-users] Re Multiple Chains

Dallas Warren Dallas.Warren at monash.edu
Thu Sep 16 03:48:21 CEST 2010

Only run pdb2gmx on a single molecule of interest, which then generates
a topology file that you can use (with slight modification) for a
simulation with a single molecule, or many.  Keep the topology to the
side and don't run pdb2gmx again.  There is no need to, you already have
the topology information for the entire molecule.  If you then add more
than one to the coordinate box, GROMACS will know from that topology how
things interact, since it is exactly the same molecule, just many copies
of it.

Then you take the coordinate file, make multiple copies of the molecule
as required, then adjust your topology file to show the correct number
of molecules.  Originally it will say 1 molecule.  If you say make a
coordinate file with a total of 8 molecules, then you will need to
change that number in the [ molecules ] section from 1 to 8 i.e.


Original .top

 [ molecules ]

Protein    1


Multiple molecule .top

[ molecules ]

Protein    8


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 11:22 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re Multiple Chains



Were all of your termini treated correctly here?  If you pass multiple
chains to 
pdb2gmx, the potential problem is that pdb2gmx will read the entire
structure as 
one protein, thus trying to connect sequential N- and C-termini.  This
is why 
the example on the wiki is pertinent - generate a topology for a single 
polypeptide, then (in your case) change the [molecules] section to
reflect the 
fact that you're building a system with 8 protein molecules (instead of
just 1). 
  Use the pdb2gmx-processed coordinate file as input into genconf and so


I'm lost :(

I have a feeling that pdb2gmx is probably converting it to one big

Procedure at this point.

genconf -f polygly.pdb -nbox 2 2 2 -shuffle  -o did_it_work.pdb

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

0: GROMOS96 43a1 force field

vi polygly.top
Changed proteins to 8

At this point I have no clue what to do....

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