AMBER Archive (2009)

Subject: Re: [AMBER] parmchk problem

From: case (
Date: Tue Aug 11 2009 - 08:51:57 CDT

On Wed, Aug 05, 2009, isaac sugden wrote:

> antechamber -i tmm_rs_rs_rr.pdb -fi pdb -o tmm_rs_rs_rr.mol2 -fo mol2

Atom names within a residue must be unique. Antechamber tries to fix this,
but that may fail when you have so many, many atoms with the same name.

Also please check carefully what is happening around atom 37. Try removing
all the long alkane chains, and just running things on the carbohydrate part.
Finally, you might want to consider using the glycam force field for this
system -- it's probably better tested for this sort of molecule than is gaff.
(Still, gaff should work with a good input pdb file.)

...good luck...dac

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