Assuming you have set up your receptor and ligand topology files as you have
described you should be able to list the ligand as you have already
described and then describe the receptor mask like this:
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 10
RSTART 41
RSTOP 100
This is how I understand it based on the descriptions in the manual for this
section.
As a side note, you could do this calculation using MMPBSA.py by supplying
the correct topology files, then the receptor and ligand masks would be
guessed by the script without the user needing to input start and stop atom
numbers or residues for either molecule. Just an idea.
Good luck!
-Bill
On Sat, May 8, 2010 at 12:15 PM, geyan <geyan.big.ac.cn> wrote:
> hello every Amber-user,
> I have simulated a complex composed of three moleculares of protein and
> one molecular of DNA.Now I got the complex's trajectory and want to
> calculate each protein's contribution to the total binding energy of the
> interaction of the proteins and DNA.
> Now the question is how to set the parameters of the MM_PBSA tutorial's
> extracting coordinate script.Specially speaking,I don't know how to deal
> with the
> NUMBER_LIG_GROUPS and the NUMBER_REC_GROUPS.In my opinion,as I want to
> calculate the single protein's contribution,I have to set this very protein
> to receptor or ligand,and let the remains to be the ligand or receptor.For
> example,if my complex has 100 atoms totally and composed like this:DNA:1-10
> atom,protein A:11-40 atom,protein B:41-70,protein C:71-100.If now I want to
> konw the detailed contribution of protein A,so in the NUMBER_LIG_GROUPS
> item,I can set it like this,
> NUMBER_LIG_GROUPS 1
> LSTART 11
> LSTOP 40
> now,the question appears,that is how to deal with the NUMBER_REC_GROUPS
> item.The remained moleculars is not single one and the atoms are obviously
> not consecutive.So does anybody know how to figure it out?
> Many thanks!
> 2010-05-08
>
>
>
> geyan
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat May 08 2010 - 20:30:03 PDT
