[gmx-users] Re Multiple Chains

Dallas Warren Dallas.Warren at monash.edu
Thu Sep 16 02:14:51 CEST 2010

Was your single molecule coordinate file energy minimised?


Did you look at the coordinate file for multiple molecules?


In your grompp step before em, what is that coordinate file you are
feeding to it?  It has a different name to the one you generated using


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 10:06 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re Multiple Chains


Sorry guys, I'm still learning the lingo.

I want to simulate multiple molecules.

This is what I tried:

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

Does this even seem like the right thing to do?

I got to this part:

grompp -v -f em -c b4em -o em -p speptide 
mdrun -v -s em -o em -c after_em -g emlog 

But I get an error that essentially tells me that my system needs to be
energy minimized:

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or
errors that give particles very high velocities you might end up with
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 150

I'm guessing I'm pretty wrong in my approach to adding multiple
molecules based on a single molecule pdb file.  I'm determined to get
this :)

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