Dear Amber Users,
I used it as below it still gives me an error :
#
DCTYPE 2
#
COMREC 5-8
COMLIG 1-4
COMPRI 1-8
RECRES 1-4
RECPRI 1-4
RECMAP 5-8
LIGRES 1-4
LIGPRI 1-4
LIGMAP 1-4
/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 , which is
the topology file of complex. Is it something to do with my trajectory file.
On the other hand I am trying to increase the number of receptor groups. I
edited the file make_crd_hg.f , NMO=100 and did make make_crd_hg .
It says make _crd_hg.f file is upto date and still my log file says as
receptor group cannot be more than 10.
Can you suggest where I am going wrong.
Thank You
John
On Thu, Jan 13, 2011 at 11:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jan 14 2011 - 11:30:03 PST
