AMBER Archive (2009)

Subject: Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz

From: Ray Luo (ray.luo_at_uci.edu)
Date: Sun Jul 19 2009 - 17:45:29 CDT

Manish,

> I was trying to use DElPHI because of two reasons,
> First, some papers say that the pbsa module of Amber is not consistence
> with the DELPHI results, but it may be true for older version.
> Second, I have learned from on the internet that pbsa module can not be
> used for charged ligand. I don't know how true it is with Amber10.
>
There were bug fixes for these issues for the earlier versions in amber
9. These fixes have been included in the Amber 10 release. However, if
you get a chance to compare pbsa with delphi and found any discrepancy,
you're welcome to report back to the list.
> However, I tried doing mm-pbsa using pbsa module of Amber and I am getting
> following error.
>
> .........................
> ........................
> Processing PB PBTOT
> Doing 1 PB PBSOL
> Doing 1 MM GAS
> No values for MM_GAS existing -> Skipping
> Processing MM GAS
> Doing 1 MM ELE
> Doing 1 MM VDW
> Doing 1 MM INT
> Doing 1 MM ELE
> Doing 1 MM VDW
> Doing 1 MM INT
> Doing 1 MM ELE
> Doing 1 MM VDW
> Doing 1 MM INT
> Processing PB PBTOT
> Doing 1 PB PBSOL
> Doing 1 MM GAS
> Doing 1 PB PBSOL
> Doing 1 MM GAS
> Doing 1 PB PBSOL
> Doing 1 MM GAS
> =>> Calc delta from raw data
> No data for 0+0 MM BOND 0
>
> I will applicate any help.
>
>
First thing first, can you reproduce the mmpbsa examples in amber10?
Note that there is an upgrade/bugfix for mmpbsa. Please patch it first
and see whether your installation works.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

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