AMBER Archive (2005)

Subject: Re: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 27 2005 - 10:08:11 CDT

On Wed, Jul 27, 2005, Arnoult, Eric [PRDFR] wrote:
>
> Can you try this leap.in ?
> "source leaprc.ff03
> source leaprc.gaff
> loadAmberPrep test_prp_resp.in
> lig = loadPdb test.mpdb
> saveAmberParm lig test.top test.crd
> quit"
>

The problem is with the pdb file, where the atom name for at 25 is in the
wrong columns:

ATOM 25 Cl25tes 1 9.155 ...

should be:

ATOM 25 Cl25 tes 1 9.155 ...

(Atom names are always in columns 13-16 of a pdb record.)

Notes:

1. After doing the loadAmberPrep step, you can type "desc tes.1", which will
show you all the atoms in the unit, with the four letter name correctly there.

2. If you do a "savePdb tes foo.pdb", you will get a pdb file where the atom
names are in the correct column.

So the real question is: how did you construct the pdb file? There may be
some place that is not correctly handling the four letter atom name in the
pdb file, but I can't say more until I know how you created this file.

...good luck...dac

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