AMBER Archive (2002)

Subject: Re: Questions about xleap and mm_pbsa(cont.)

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 23 2002 - 12:18:44 CDT

On Tue, Jul 23, 2002, Salinthip Thipayang wrote:
> >
> > > mutant2 = loadpdb "./mutantGLN_b4_xleap2.pdb"
> > Loading PDB file: ./mutantGLN_b4_xleap2.pdb
> > -- residue 10240: duplicate H1 atoms (total 10)
> > -- residue 10240: duplicate H2 atoms (total 10)
> > -- residue 10240: duplicate O atoms (total 10)

So, what do the lines the the above pdb file look like around residue
10240?? The LEaP message is pretty specific: it doesn't like this residue
(and a lot of others). Play around with the pdb file (e.g. remove all
residues beyond the first one LEaP complains about, then try to load that
file). You need to narrow down the problem until you can figure out what
is happening.

It won't do any good, given above message, to have LEaP save a pdb file
(or to examine any pdb file leap might create at this point.) You have to
figure out what is going on with the *input* pdb file.

[I would repeat my recommendation to use ambpdb -- couldn't tell from your
mail whether you had tried this or not.]

..good luck...dac 

-- 

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