Jason,
I think this is because you're using sander. Could you use pbsa instead
for future releases of MMPBSA? That's why pbsa was created in the first
place.
Qin is working to revise the PB routines in sander so we can run MD/MIN
with the new PB force routines. After his changes, the PB routines in
sander will be optimized for MD/MIN. The default options are also
changed to suit the new purpose, which is the cause of the bomb in your
test.
Qin is also in the process of copying Holger's features from sander to
pbsa. So if you want to support those decomposition and hybrid water
functions via pbsa, they will be there very soon.
Let me know if there is any problem generating the new &cntrl list for
pbsa. It's much simpler now.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
Jason Swails wrote:
> Hello,
>
> It appears as though some changes have been made in the PBSA that have
> broken input files we've been using for MMPBSA. The input file is
> shown below, along with the error in the mdout that it gave. Any
> ideas?
>
> ---------------------------------------------------------------------------------------------
> File generated by MMPBSA.py
> &cntrl
> ntb=0, igb=10, cut=999.0, nsnb=99999,
> imin=5, maxcyc=0, cutcap=-1, xcap=0,
> ycap=0, zcap=0, idecomp=0, ntpr=1,
> ivcap=0, ntmin=2,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=100.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
> npopt=1, cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4,
> /
> ---------------------------------------------------------------------------------------------
>
> And the sander mdout errors:
> ---------------------------------------------------------------------------------------------
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> PB Info in pb_read(): igb has been overwritten by ipb
> PB Info in pb_read(): npopt has been overwritten with inp
> PB Bomb in pb_read(): use of radi other than vdw sigma for
> np solvation dispersion/cavity is not supported!
>
> ---------------------------------------------------------------------------------------------
> Thanks,
> Jason
>
>
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Received on Fri Feb 05 2010 - 14:00:03 PST
