[gmx-users] Re Multiple Chains

[Dallas Warren]

Talk of each chain you have there as a molecule, which is what they are.
So what you want is multiple molecules within the box, correct?

 

 Once you start referring to them at molecules, then it should become
far more obvious what you need to do.  To do that, you take a single
molecule in a coordinate file, then tell a script to put many copies of
that molecule within a given box size.  The GROMACS scripts to date have
not really been the best for doing that, but genconf and genbox are the
ones that you can use.

 

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 8:32 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re Multiple Chains

 

"""

This depends entirely upon what your goal is.  Your original question
implied 
you wished to build a system of multiple, identical peptides, pertaining
to:
 
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_c
hains
 
Now you want a multimeric protein for which there are multiple,
potentially 
different peptide, i.e.:
 
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Non-identic
al_chains
 
The approaches are completely different, as the documentation should
make quite 
clear.  Simply "having multiple chains" is a very vague statement.
Perhaps if 
you clearly stated your goal for the simulation I (or someone else)
could help 
you better.
 
As for the PDB site, there are probably thousands of proteins in line
with what 
you want.  Any heteromultimeric protein would do (assuming, of course,
the 
latter case of non-identical chains).
 
-Justin

"""





Sorry I wasn't clear.  Basically I want to have a simulation box with as
many of the same polypeptide as I can cram in, essentially a simulation
of the polypeptide melted.

I would like to see how the polypeptides interact with each other with
the ultimate goal of simulating block copolymers.  Since I'm new with
Gromacs, I'm just trying

to figure out how to run simulations with multiple chains where all
chains are the same type.



Justin, you've been very helpful so far and I appreciate it. 
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