Dear all,
I'm using MMPBSA.py in Ambertools12 for free energy binding
calculations. I use cpptraj to generate separate prmtop files
(complex.prmtop, rec.prmtop and lig.prmtop) by stripping different
parts of the trajectory. FYI, my original prmtop file used for MD runs
is from CHAMBER.
For GB and nmode parts, the calculations were done successfully but
for PB and decomp, the program ended with the error:
CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
rec_lig.prmtop! (rec_lig.prmtop is my complex.prmtop)
and this is the output from _MMPBSA_complex_pb.mdout.0
Reading parm file (rec_lig.prmtop)
title:
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=0.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.037800
mm_options: cavity_offset=-0.569200
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB frms
eff.c(2660) enb14 --> 1875.427
eff.c(2661) eel14 --> 8737.616
i then try to set used_sander=1, program ended with the same error and
output file:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 06/06/2012 at 16:17:18
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_pb.mdin
| MDOUT: _MMPBSA_complex_pb.mdout.0
|INPCRD: _MMPBSA_dummycomplex.inpcrd.1
| PARM: rec_lig.prmtop
|RESTRT: _MMPBSA_restrt.0
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd.0
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, dec_verbose=0, ipb=2,
ntb=0, cut=999.0, imin=5, inp=2,
igb=10,
/
&pb
maxitn=1000, fillratio=4.0, radiopt=1,
/
error in reading namelist cntrl
For decomp, the program ended with the same error as well, with the output:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 06/06/2012 at 16:12:12
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_gb_decomp_com.mdin
| MDOUT: _MMPBSA_complex_gb.mdout.0
|INPCRD: _MMPBSA_dummycomplex.inpcrd.1
| PARM: rec_lig.prmtop
|RESTRT: _MMPBSA_restrt.0
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd.0
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, ntb=0, surften=0.0072,
extdiel=80.0, ncyc=0, cut=999.0,
gbsa=2, saltcon=0.15, imin=5,
idecomp=2, igb=5,
/
Residues considered as REC
RRES 1 264
END
Residues considered as LIG
LRES 265 265
END
Residues to print
RES 1 265
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 06/04/12 Time = 16:08:54
NATOM = 4304 NTYPES = 67 NBONH = 2175 MBONA = 2188
NTHETH = 4881 MTHETA = 2995 NPHIH = 8137 MPHIA = 3894
NHPARM = 0 NPARM = 0 NNB = 23795 NRES = 265
NBONA = 2188 NTHETA = 2995 NPHIA = 3894 NUMBND = 105
NUMANG = 221 NPTRA = 404 NATYP = 67 NPHB = 0
IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
NCOPY = 0
rdparm: a parameter array overflowed
(e.g. the table of dihedral params)
NUMBND = 105 max is 5000
NUMANG = 221 max is 900
NPTRA = 404 max is 1200
NATYP = 67 max is 100
NPHB = 0 max is 200
NTTYP = 2278 max is 1830
I'm not sure what is the problem with my complex.prmtop, and why GB
and nmode calculations can be done with the same prmtop file but not
the PB and decomp.
Pls advise.
Thanks and regards,
colvin
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Received on Wed Jun 06 2012 - 02:00:03 PDT
