AMBER Archive (2003)

Subject: Re: antechamber and its prepin files

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 19 2003 - 15:08:55 CST

On Wed, Feb 19, 2003, Steve Seibold wrote:

> I am constructing ligands to use in AMBER. My problem is that when I build
> a simple molecule (carbon, hydrogen and oxygen) using some program (e.g.
> MOE) that will output a pdb file ANTECHAMBER is not able to convert it into
> a correct prepin file. I have tried, successfully a few times, to rename the
> carbon atoms from C to CA etc. Most of the time it takes hours (to days) for
> me to locate something that will make a correct prepin file to load into
> xleap. I keep getting carbon atoms and hydrogens referred to as DU in my
> prepin files (along with nan0x7ffffffff). Is there some logical format that
> I can use to convert my pdb files to a prepin file without this trouble? I
> would appreciate any help in this area.

Please send an example pdb file that fails. You might look at the pdb
files in the subdirectories under $AMBERHOME/test/antechamber, to see if you
can spot any way in which your pdb files are different from those there.
(I'm assuming that you have run the antechamber tests, and they work OK).

The names of the atoms are not supposed to make any difference, so some other
problem must be occurring.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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:                   
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