AMBER Archive (2005)

Subject: Re: AMBER: Problem with xleap

From: FyD (fyd_at_u-picardie.fr)
Date: Wed May 11 2005 - 21:21:12 CDT

In some cases, LEaP add unwanted atoms for some particular residue _names_...
Bugs ? Or even do not accept some atom names...
Try to change the residue name/file name...
Regards, Francois

> I have a question regarding xleap. It is about the AMBER's libraries, and
> something strange is happening when I am trying to do the following:
>
> I start 'xleap'. Then;
>
> > source leaprc.ff99
> > savepdb RC rc.pdb
> > quit
>
> Now, I see the file 'rc.pdb' in the directory. Then I start 'xleap' again;
>
> > source leaprc.ff99
> > molecule = loadpdb rc.pdb
>
> and xleap adds 2 atoms!!! Here is what xleap is giving me after I load the
> rc.pdb:
>
> > molecule = loadpdb rc.pdb
> Loading PDB file: ./rc.pdb
> Created a new atom named: O2* within residue: .R<RC 1>
> Created a new atom named: HO*2 within residue: .R<RC 1>
> Added missing heavy atom: .R<RC 1>.A<O2' 29>
> total atoms in file: 31
> Leap added 2 missing atoms according to residue templates:
> 1 Heavy
> 1 H / lone pairs
> The file contained 2 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
>
> Question: I have saved the .pdb structure according to the AMBER' residue
> library, and when I try to open the same .pdb in xleap, it adds two atoms
> (saying that they are missing, even though they are not!). Am I missing
> something here? Thanks in advance for your responses. 

-- 
  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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