AMBER Archive (2008)

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

From: Alan (alanwilter_at_gmail.com)
Date: Wed Jul 16 2008 - 07:46:15 CDT

I am very curious to know which antechamber version are you using
because I never see option '-mk'.

Would be '-gk' (could be '-ek', but your quoted string is not for mopac AFAIK).

Cheers,
Alan

On Wed, Jul 16, 2008 at 1:15 PM, SeungPyo Hong <sp1020_at_gmail.com> wrote:
> 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 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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