AMBER Archive (2003)

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

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Tue Jul 15 2003 - 16:01:47 CDT

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
> >
> >
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu