Dear all,
I want to use CHARMM force field to carry out binding free energy
calculation through MMPBSA python script in AmberTools1.5. Using the
Chamber program, the corresponding " prmtop " files are generated. And then
use the following input file to calculate binding free energy:
*&general*
* startframe=1, endframe=1, interval=1,*
* keep_files=1,strip_mdcrd=0,verbose=1,*
* use_sander=1*
*/*
*&pb*
* istrng=0.1*
*/*
But calculation is interrupted due to sander error during PB calculations.
the error message in the _MMPBSA_complex_pb.mdout file is:
rdparm: a parameter array overflowed
(e.g. the table of dihedral params)
NUMBND = 133 max is 5000
NUMANG = 297 max is 900
NPTRA = 612 max is 1200
NATYP = 72 max is 100
NPHB = 0 max is 200
*NTTYP = 2628 max is 1830*
**
Amber 11 and AmberTools 1.5 are used in the calculation.
Would you like to help me with this problem? Thanks in advance!
Best wishes,
Yours Sincerely,
Duan Baogen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 06 2012 - 18:30:03 PST
