Dear amber developers and users.
I need to read scee and scnb from topology file in NAB. So I revised source files to set up pointers to store the variable 1-4 scaling arrays in the parm struct (AmberTools/src/sff/sff.h).
> sff.h
typedef struct parm {
REAL_T *Gvdw, *Scee, *Scnb;
}
Also SCEE_SCALE_FACTOR and SCNB_SCALE_FACTOR set up in prm.c file(AmberTools/src/sff/).
> prm.c
/*
* READ Scee -Scee
*/
pfind(file, newparm, "SCEE_SCALE_FACTOR");
for (i = 0; i Nptra; i++) {
if (get_mytaskid() == 0) {
#ifdef NAB_DOUBLE_PRECISION
fscanf(file, " %lf", &prm->Scee[i]);
#else
fscanf(file, " %f", &prm->Scee[i]);
#endif
}
}
#if defined(MPI) || defined(SCALAPACK)
MPI_Bcast(prm->Scee, prm->Nptra, MPI_DOUBLE, 0, MPI_COMM_WORLD);
#endif
skipeoln(file);
/*
* READ Scnb -Scnb
*/
pfind(file, newparm, "SCNB_SCALE_FACTOR");
for (i = 0; i Nptra; i++) {
if (get_mytaskid() == 0) {
#ifdef NAB_DOUBLE_PRECISION
fscanf(file, " %lf", &prm->Scnb[i]);
#else
fscanf(file, " %f", &prm->Scnb[i]);
#endif
}
}
#if defined(MPI) || defined(SCALAPACK)
MPI_Bcast(prm->Scnb, prm->Nptra, MPI_DOUBLE, 0, MPI_COMM_WORLD);
#endif
skipeoln(file);
I need to know more details after above procedures.
And I saw related mail by Jason in University of Florida. He said that I need to modify the 1-4 calculation in the nbond() routine of AmberTools/src/sff/sff2.c(There is only nbond2() routine. Is it right?) to use these values instead of scee (which is passed in as eelfac and enbfac). I would like to know more about it.
One more question, how to revise rgbmax in mmpbsa.py?
Thank you.
Lee
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Received on Tue Sep 25 2012 - 05:30:03 PDT
