[gmx-users] Fwd: gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 13 22:07:50 CEST 2008

---------- Forwarded message ----------
From: He, Yang <yang.he at mavs.uta.edu>
Date: Mon, Oct 13, 2008 at 5:35 PM
Subject: gromacs
To: "tsjerkw at gmail.com" <tsjerkw at gmail.com>

Hi ,

I am using the gromcas to simulate the course grain for DNA. I listed
the new atom types in the .atp file like this

 Ab  134.1;   Adenine base
 Tb  125.1;   Thymine base
 S   83.11;   Sugar
 P   94.97;   Phosphate

But when I run this, it always showa that Atomtype 'Ab' not found! and
Twin-range neighbour searching (NS) with simple NS algorithm not

I wonder whether you can give me some suggestions about how to solve
the problems.

Also, can you tell me how to define the potential functions which is
not inlucded in the gromacs in the files.

Thank you for your possible reply.


Yang He

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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