Hello,
These parameters are explained in the Amber manual. COMREC are the complex
residues that are part of the receptor. COMLIG are the complex residues
that are part of the ligand. COMPRI are the residues that you wish to print
out. RECRES are the receptor residues in the receptor prmtop (You can just
put all of the receptor residues, i.e. 1-# residues in receptor), RECPRI are
the receptor residues in the receptor prmtop that you wish to print, and
RECMAP are the equivalent residues in the *complex* topology file that
correspond to the residues RECPRI in the receptor topology file. LIGRES,
LIGPRI, and LIGMAP are analogous to the ligand.
You have
COMREC 5-8
COMLIG 1-4
COMPRI 1-8
What this means is that your ligand is at the beginning of your complex
prmtop file; so you have a 4-residue ligand (or larger if you have more than
8 residues in your system). The receptor residues are the four residues
5-8. You would like to print out all 8 residues (1-8). If this is correct,
then the other variables should be
RECRES 1-4
RECPRI 1-4
RECMAP 5-8
Because you are only printing the first 4 (or only 4?) residues of your
receptor according to what you specified in your COMREC variable above, and
you are printing all 4 of these. However, residues 1-4 in the receptor
prmtop map to residues 5-8 in the complex prmtop, hence the value for
RECMAP. Likewise, for the ligand you have
LIGRES 1-4
LIGPRI 1-4
LIGMAP 1-4
Hope this helps,
Jason
On Thu, Jan 13, 2011 at 10:22 PM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users,
>
> I am using MMPBSA_Decomp_Residue
>
> DCTYPE 2
> #
> COMREC 5-8
> COMLIG 1-4
> COMPRI 1-8
> RECRES 1-4
> RECPRI 1-4
> RECMAP 1-8
> LIGRES 1-4
> LIGPRI 1-4
> LIGMAP 1-4
>
>
> It gave me error as /usr/local/apps/amber9/exe/sander -O -i sander_com.in-o
> sander_com.1.out -c ./snap_com.crd.1 -p ../../prmtop/poly_1.prmtop not
> successful
>
> The specifications LIGPRI, LIGRES and RECPRI , RECRES , do they imply
> number
> of residues or the residue numbers of topology file.
>
> I appreciate your suggestions.
>
> Thanks
> John
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 13 2011 - 20:30:02 PST
