AMBER: Ligand force field generation, and its consistency with the force field of the protein.

From: SeungPyo Hong <sp1020.gmail.com>
Date: Wed, 16 Jul 2008 21:15:48 +0900

Dear Amber users,

I want to perform MD simulation with a ligand, however I don't know whether
I am going to the right direction.
Any command of yours will be a great help for me.

I need to generate force field of ligands, and made one using the following
commands:

 $ antechamber -i DRGML2.TOPH -fi mol2 -o ligand.prepin -fo prepi -c bcc -s
2 -nc -4 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=BFGS XTEST=0.0001
MAXOPT=20000"

$ parmchk i lipid_a.prepin f prepi o ligand.frcmod
 * The charge of the ligand is '-4'.
* As many had already noticed, the 3D structure is generated from DUNDEE
PRODRG server.

However, I just remember that the consistency of the force field is
important.
I will use AMBER03 FORCE FIELD in the simulation.

However, I don't know whether the AM1 can be used with AMBER03 force field,
because as I remember AMBER03 force field was generated with more
complicated methods and basis functions.

Sincerely,
Seungpyo Hong
-- 
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'At the same time, he allowed interaction among objects.'
-Seungpyo Hong
Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_.kaist.ac.kr
sp1020.gmail.com
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Received on Sun Jul 20 2008 - 06:07:09 PDT
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