AMBER Archive (2002)

Subject: Re: MM-PBSA: .crg file for Delphi

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Dec 11 2002 - 12:31:07 CST

Thomas Steinbrecher wrote:
>
> Dear AMBER users,
>
> I plan to do an MM-PBSA calculation on a protein/ligand
> complex I simulated with the ff99-force field.
> I wonder what .crg-file for Delphi I should state in my
> input script.
> The AMBER manual states on p.18 that the ff99 force field
> uses the partial charges from the Cornell et al. force
> field (ff94) parameters.
> So I thought I could use the my_amber94_delphi.crg file
> provided with mm-pbsa for the partial charges of my amino
> acids and just add the ligand partial charges to it.
>
> Is this a reasonable approach or do I have to prepare my
> own .crg file and if I have to, how do I do this?

Yes, this is reasonable. Be careful also to use the appropriate charges
for the N- and C-terminus. In the my_amber94_delphi.crg file from the
Example directory, you need to adjust the charges (and residues) at the
beginning of the file for this. You can find information about these
charges in the $AMBERHOME/dat/leap/lib/all_amino{nt,ct}94.lib files.
Related *.lib files will also be helpful if you want to compile your own
*.crg file for mm_pbsa.

> My second question is this:
>
> In the mail reflector it is stated that I have to prepare 3
> different crd and prmtop files for lig, com and rec, even
> if I only did one MD-simulation. Can I create this files by
> just using ptraj to strip all residues but the ones
> corresponding to ligand or receptor or complex?

This is one way. Write out snapshots as restrt files then.
Alternatively, you can use the GenerateCoordinates (GC) option in the
mm_pbsa.in file, along with information provided in the @MAKECRD
section.

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++