[AMBER-Developers] recent PB changes?

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 5 Feb 2010 13:16:30 -0500

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

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Feb 05 2010 - 10:30:03 PST
Custom Search