Re: AMBER pdb help - lost atoms

From: David A. Case <>
Date: Tue, 1 Apr 2003 12:19:35 -0800

On Tue, Apr 01, 2003, wrote:

> I've been able to get through from creating a molecule to running MD in
> sander, but it turns out some of my atoms in the initial file are getting
> "lost". Somewhere between the conversion from pdb to prepin file, my file
> goes from 54 atoms down to 24 atoms. This was noted by D. Case - he
> thought I had a 24 atom system, but I initially had a 54 atom system. The
> remaining atoms get listed as "Unrecognized atomic name X, exit" and
> end up having zeroes for x, y, and z, and charge in the pdb.

One possibility is that the atom names are not unique. Every atom within
a given residue has to have a unique name, since LEaP will ignore duplicates.

Also, what program is giving you the above error message?

The general "do" for leap is this: keep editing your input pdb file until
LEaP no longer complains. Pay careful attention to any messages you get
when invoking the loadPdb command. Use the xleap viusalizer to see if the
unit you have loaded in looks correct (use the bondbydistance command if you
don't have standard residues).

...good luck...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
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Apr 01 2003 - 21:53:00 PST
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