Re: tleap in large systems

From: David A. Case <>
Date: Thu, 27 Mar 2003 12:43:01 -0800

On Wed, Mar 26, 2003, GUILLERMINA L ESTIU wrote:
> I am using amber6. I am dealing with a large system that has 47000 residues
> (water box included)
> When using tleap the top and crd files are not built properly.
> Tleap does not complain, but when trying to use them in the minimization
> (sander) I got a message FATAL: NATOM mismatch in coord and topology files

Amber 6 was not set up very well to handle systems with more than 100000
atoms, even though tleap does not complain.

The easiest thing to do is to upgrade to amber 7. Alternatively, you can
modify the section (in routine getcor) that reads the number of atoms. It
probably needs to use an I6 rather than an I5 format to correctly read the
input files you have.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Mar 27 2003 - 20:53:01 PST
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