AMBER Archive (2009)

Subject: Re: [AMBER] xleap input pdb problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed May 06 2009 - 21:16:10 CDT

On Wed, May 06, 2009, Majeed Shaik wrote:
>
> I am trying to load a pdb file of a non-standard residue into xleap. After I
> load the mol2 and frcmod file into xleap I load the pdb file and the
> conformation is completely different to the actual conformation of the input
> pdb file. I am attaching the mol2, frcmod, input pdb file here.I cannot
> understand what's the problem with files.

You probably(?) got lots of errors during the loadPdb command, since the atom
names in the oct.pdb file are nothing like the atom names in the FLE.mol2
file. Note the all atom names in a given residue must be unique, and the atom
nmaes in the pdb file have to match the atom names in the mol2 file.

...dac

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