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

From: Arnoult, Eric [PRDFR] <>
Date: Wed, 27 Jul 2005 17:59:43 +0200

Dear Dr. Case,

I construct the pdb file with the following command lines :


${AMBHOME}/antechamber -i ${PREPDIR}/${MOL}.mol2 -fi mol2 -o ${MOL}.ac -fo
ac -j 5 -c bcc -nc ${CHARGE} -at ${ATMTYPE} -s 2 -rn ${MOL}
${AMBHOME}/antechamber -i ${MOL}.ac -fi ac -o ${MOL} -fo prepi
${AMBHOME}/antechamber -i ${MOL}.ac -fi ac -o ${MOL}.mpdb -fo mpdb -j 5 -s 2
-rn ${MOL}
${AMBHOME}/antechamber -i ${MOL}.ac -fi ac -c wc -cf ${MOL}.crg
${AMBHOME}/parmchk -i ${MOL} -f prepi -o frcmod${MOL}.par

May be I do a mistake in these command lines, I don't think so



-----Original Message-----
From: []On Behalf
Of David A. Case
Sent: Wednesday, July 27, 2005 5:08 PM
Subject: Re: AMBER: An atom name with 4 characters is not compatible
with Leap ?

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


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

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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Received on Wed Jul 27 2005 - 17:53:00 PDT
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