AMBER Archive (2003)

Subject: Re: AMBER: Questions about mm_pbsa and alanine scanning

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Wed Jul 16 2003 - 08:04:30 CDT

Hi there,

I got it figured out by myself. The problem lies in LSTOP, not in four
variables of "MUTANT_".

Haizhen

On Tue, 15 Jul 2003, Haizhen Zhong wrote:

> Hi Tatasja,
>
> I DO use the topology files for the mutant system. I did it different way.
> I first mutated residue to ala in MOE and then generated the topology
> files in leap. I believe both ways should give the same topology files.
> When I check the leap generated topology (and its inpcrd files) using
> carnal, it gives the correct mutated system. So the problem does not lie
> in the topology files, but in the definition of the "MUTANT_KEEP". And I
> don't understand why using the carbonyl carbon (C of C(O)) as
> "MUTANT_KEEP". It dones nothing to the mutated center. But I followed the
> instructions and got the error message asking for checking
> anal_complex.1.out which stated topology and crd files have different atom
> numbers.
>
> If anyone can provide more help, I will highly appreciate your help!
>
> Haizhen
>
> On Tue, 15 Jul 2003, Natasja Brooijmans wrote:
>
> > When you do alanine scanning, you need to generate topology files for the
> > mutant system with leap before you run the mmpbsa scripts.
> >
> > Good luck,
> >
> > Natasja
> >
> > Natasja Brooijmans, Ph.D.
> > Visiting Post-Doctoral Scholar
> > Kuntz Laboratory
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > San Francisco, CA 94143-2240
> > phone: 415-476 3986
> > fax: 415-502 1411
> > e-mail: nbrooij_at_itsa.ucsf.edu
> >
> > On Tue, 15 Jul 2003, Haizhen Zhong wrote:
> >
> > > Dear Amber users,
> > >
> > > I'm very interested in using the computational Alanine scanning technique
> > > described in mm_pbsa munual. Yet I've found it's hard to understand some
> > > of the scripts in the mm_pbsa file. I've had the correct topology files
> > > for the mutants. According to the definitions of "MUTANT_ATOM1",
> > > "MUTANT_ATOM2", "MUTANT_KEEP", and "MUTANT_REFERENCE", I modified the
> > > input files exactly according to the definitions. Unfortunately, after
> > > running mm_pbsa, I got "FATAL: Topology and coord files do not match" in
> > > my anal_complex.1.out file. After checking the coordinate files from
> > > complex, protein, and ligand (a small peptide, mutation was on this small
> > > peptide) with respective prmtop files, I found the atom numbers were
> > > different between the crd file and the prmtop file. I believe the problem
> > > lies in the definition of the above four variables. Among these four,
> > > "MUTANT_ATOM1" and "MUTANT_REFERENCE" are clear and easy to understand.
> > > Therefore the most problem may be in the definition of "MUTANT_ATOM2" or
> > > "MUTANT_KEEP" (especially "MUTANT_KEEP").
> > >
> > > Worthy to mention is that if you look at the example provided in the
> > > amber6 mm_pbsa for the alanine scanning for residues in p53, you can find
> > > the numbers for the above four variables contradictory with each other in
> > > terms of Thr18, Phe19 and Trp23 mutated to Ala (line 584 to line 596 in
> > > mm_pbsa script in amber6 version).
> > >
> > > Can anyone clarify my confusion and help me with the alanine scanning
> > > using mm_pbsa?
> > >
> > > Thank you very much for your help!
> > >
> > > Haizhen
> > >
> > >
> > >
> > >
> > >
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> > >
> >
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