Re: Chains, LEaP and ambpdb

From: David A. Case <>
Date: Tue 17 Dec 2002 13:09:48 -0800

On Tue, Dec 17, 2002, Luis Gracia wrote:
> I constructed a system with LEaP that has more than 10000 waters. When
> converting the files to pdb with the program ambpdb I get **** in the
> residue number from 10000 up.

This is not supposed to happen. Do you have amber7? When I run ambpdb
on a system with lots of waters (say in the benchmarks/rt_polymerase
directory), I get a pdb file where the residue numbers "start over" again
every 10000 residues. This file can then be read back into LEaP with no

So, basically, we need more detailed information to find out what is going
wrong for you.


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 Tue Dec 17 2002 - 13:09:48 PST
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