Re: [AMBER] AMBER parameters for caffeine molecule

From: arikcohen <>
Date: Wed, 21 Dec 2011 22:58:47 -0800


One option is to use an electronic structure program such as Gaussian
and to do the following:

1. Run a single point calculation on your substrate/ligand/inhibitor as
in the following example which is taken from Gaussian03,

# hf/6-31g(d) maxdisk=50000MB geom=connectivity density=current
iop(6/33=2,6/42=6) pop=mk scf=tight


0 1
C 38.88300000 36.19500000 39.46000000
N 38.79800000 37.19600000 44.43300000
O 38.04700000 34.21600000 39.83700000

2. Run the following Amber util programs in the following order:
a. antechamber -i FILENAME.out -fi gout -o FILENAME.prepin -fo prepi -c
b. parmchk -i FILENAME.prepin -fi prepi -o FILENAME.frcmod
Warning: if .frcmod file includes the line: NEEDS ATTENTION, this means
that no parameters were found for a particular bond, angle, or dihedral
and you need to enter them manually.
c. antechamber -i FILENAME.prepin -fi prepi -o FILENAME.pdb -fo pdb

I hope this helps,


On 12/21/2011 9:26 PM, Bhanita Sharma wrote:
> Dear all,
> I am doing a project on Caffeine simulation, and for this I
> needed all the force field parameters for Caffeine molecule. I am new to
> this field. Can someone help me in my work..?
> Thanks..
> _______________________________________________
> AMBER mailing list

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Received on Wed Dec 21 2011 - 23:00:02 PST
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