AMBER Archive (2004)

Subject: AMBER: antechamber gives GDP 0 charge

From: Raik Grünberg (
Date: Wed May 05 2004 - 15:17:53 CDT

Hi there,

I just tried to create parameters for GDP and GTP using antechamber (Amber 7).
Everything sort of worked but antechamber seemed to not only ignore the
"-nc -3" parameter but actually assigned charge 0.0 to all atoms.
It's the first time that I am using it, perhaps I made some obvious mistake.
Here is the command:

antechamber -i GDP_in.pdb -fi pdb -o GDP.prep -fo prepi -nc -3 -rn GDP -at
amber -c resp

GDP_in.pdb was prepared from the X-ray structure. I deleted the addidtional P,
added hydrogens in tleap and added back the P.

parmchk -i GDP.prep -f prepi -o frcmod.gdp
gives a frcmod in which some bond angles are marked as missing, although they
are existing in the parm99.dat. I just copied them over from parm99.dat.

tleap loads the prep and then the PDB without trouble but all the atoms have 0
charge. Any ideas anyone, what could have gone wrong?

Or alternatively, has anyone already parameters ready for GDP / GTP?

Many thanks!

Raik Grünberg | Bioinformatique Structurale
                                | Institut Pasteur
Tel: +33/ | Paris, France
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