Thanks, Jack. Does AMBER8 include this module or I have to use AMBER7?
Lei
Jack Lei wrote:
> Anal could do it.
>
> Jack
>
> On Tue, 15 Mar 2005 14:45:47 -0500, lei jia <jial.broyde.nyu.edu> wrote:
> > Dear Amber users,
> >
> > I am using MM-PBSA generated sander input file to calculate the
> > component interactions of a group of atoms. I had no problem to
> > calculate them on the residue level by using the RES card. I wonder if I
> > can do that on the atom level by using the ATOM card in the group
> > specification section. If not, what can I do to calculate the
> > interactions between the whole molecule and several atoms belong to the
> > molecule. Thanks a lot!
> >
> > Lei
> >
> > Here are my input files and error messages from the output:
> > #############################################################
> > File generated by mm_pbsa.pl. Using MM
> > &cntrl
> > ntf = 1, ntb = 0, dielc = 1,
> > idecomp= 1,
> > igb = 2, saltcon= 0,
> > offset = 0.09, extdiel= 78.5,
> > gbsa = 0, surften= 1.0,
> > cut = 99999.0, nsnb = 99999,
> > scnb = 2.0, scee = 1.2,
> >
> > imin = 1, maxcyc = 1, ncyc =0,
> > &end
> > Residues considered as REC
> > RRES 1 22
> > END
> > Residues to print
> > ATOM 173 182
> > END
> > END
> > ######################################################
> > ----- READING GROUP 2; TITLE:
> > Residues to print
> > ***PROBLEMS WITH GROUPATOM 173 182 0 0 0 0 0
> > 0 0 0 0 0 0 0*******
> >
> > Number of atoms in this group = 0
> >
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Received on Wed Mar 16 2005 - 02:53:01 PST
