Re: Chains, LEaP and ambpdb

From: Luis Gracia <>
Date: Tue 17 Dec 2002 16:23:55 -0500

David A. Case wrote:
> 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
> problems.
> So, basically, we need more detailed information to find out what is going
> wrong for you.
> ..regards...dac


sorry, I forgot to say that I am using amber 6. I also just got the new
ptraj-6.4 and I get the same result: '****' instead of the residue
number. I guess this is fortran telling that it cannot fill the 5 digit
residue number in a 4 digit field.

Thanks for the help,

kind regards, Luis

Luis Gracia, PhD
Dept. Physiology & Biophysics, 21-280
Mt Sinai School of Medicine
One Gustave L. Levy Place, New York NY 10029
Tel: (212) 241-0858   ---   Fax: (212) 860-3369
Received on Tue Dec 17 2002 - 13:23:55 PST
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