Dear Amber users,
I am using the MMPBSA.py.MPI on a protein with a modified amino acid and the log file is giving the following error:
CalcError: /opt/asn/apps/amber12_tools13/amber12/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
The same calculation for the protein without the modified residue is working!
Furthermore, the _MMPBSA_complex_pb.mdout.0 file is giving the below error:
Reading parm file (complex.prmtop)
title:
default_name
Parameter topology includes 10-12 terms:
These are assumed to be zero here (e.g. from TIP3P water)
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=100.000000
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
Error: ipb>0 is incompatible with periodic boundary conditions.
Error: To use this method set IFBOX in the PRMTOP file to 0.
Error: See http://ambermd.org/formats.html
Please help for i can not figure the way to deal with it.
Thanks,
Symon
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Received on Thu Oct 10 2013 - 13:00:07 PDT
