AMBER Archive (2008)

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

From: SeungPyo Hong (sp1020_at_gmail.com)
Date: Wed Jul 16 2008 - 07:15:48 CDT

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__at_kaist.ac.kr
sp1020_at_gmail.com

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