Re: [AMBER] questions about thermodynamic integration atom name and order

From: 千语千寻 <>
Date: Mon, 29 Oct 2012 22:59:04 +0800


2012/10/29 Yulin Huang <>

> Dear Amber users:
> I am performing binding free energy calculation for a kinase with
> 12 ligands using thermodynamic integration (AMBER11). It seems that the
> atom names and orders for the corresponding atoms in these 12 ligands in
> the initial setup have to be the same. Thus the
> parm files and crd files generated after I use the antechamber, parmchk
> could be the same
> for the corresponding atoms. After that, the small mask (one or two atoms)
> can be specified for calculations.
> I have manually made all the corresponding atom names the same. Now I am
> trying to make the order the same. It is not an easy task. The way I do is
> to put all the different atoms among 12 ligands at the end of ligand mol2
> files. But I have to change all the connectivity part. I've tried to load
> the mol2 file into software MOE and output the pdb file and then convert to
> mol2 file. But the different atom such as O will be placed in the middle
> of the mol2 file automatically. But I have to put the different atoms in
> the end to make the corresponding atoms in the same order.
> Does anyone has any ideas for this problems? Many thanks in advance.
> --
> Yulin "Joyce" Huang
> Ph.D Candidate
> Computational Chemistry (CADD)
> Advisor: Dr. Robert C. Rizzo
> State University of New York at Stony Brook
> Stony Brook NY,11790
> Office: (631)632-8519
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Oct 29 2012 - 08:00:06 PDT
Custom Search