[gmx-users] Error in using gromacs for MD simulation

Dallas Warren Dallas.Warren at monash.edu
Fri Apr 27 02:08:01 CEST 2012


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 9903 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 vineetha mandlik
Sent: Tuesday, 24 April 2012 7:56 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Error in using gromacs for MD simulation

---------- Forwarded message ----------
From: Rossen Apostolov <rossen at kth.se<mailto:rossen at kth.se>>
Date: Mon, Apr 23, 2012 at 11:53 PM
Subject: Re: error in using gromacs for MD simulation
To: vineetha mandlik <vinee2here at gmail.com<mailto:vinee2here at gmail.com>>

Please send your questions to the mailing list gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>. This is the administrative mail.


On 2012-04-23 17.12, vineetha mandlik wrote:
Respected Sir,

   Thanks for your reply. I had written to you previously regarding the error in the grompp command when running the MD simulation of a protein, structure was obtaining using homology modelling approach.

The error reported was : Number of coordinates in coordinate file (z_b4em.gro) does not match that of topology file (z.top). We are however not able to run the nohup command because of the above mentioned error.  I m sending you the pdb,top and gro files along with a file containing the commands and output obtained.

Your help in resolving this issue would be highly appreciated.

Thanking you.

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