Hi,
I am trying to run MMPBSA.py with -make-mdins flag so that I can modify the
mdin files for use with membrane proteins and also carry out the
per-residue decomposition. I am using the following input file:
Input file for PB calculation MMPBSA with membrane proteins from the manual
with recommended parameters like ipb=1:
<<<
&general
use_sander=1,
startframe=1, endframe=5, interval=1,
keep_files=2, netcdf=1, debug_printlevel=2
/
&pb
istrng=0.150, bcopt=10, fillratio=1.5,
mthick=36.8555, mctrdz=0, indi=2.0,
eneopt=1, nfocus=1, inp=1, cutfd=7.0, cutnb=99.0,
ipb=1, npbverb=1, solvopt=2, radiopt=0,
maxarcdot=15000, poretype=0,
memopt=1,
/
&decomp
dec_verbose=3, idecomp=2,
/
>>>
but MMPBSA.py with -make-mdins flag gets rid of memopt option and other
options from the original &pb section and also sets ipb=2. It produces
three mdin files (complex, receptor, ligand). Here is the complex input
file produced: _MMPBSA_pb_decomp_com.mdin
<<<
File generated by MMPBSA.py
&cntrl
ntb=0, nsnb=99999, cut=999.0,
ioutfm=1, imin=5, igb=10, idecomp=2,
ipb=2, inp=1,
/
&pb
epsin=2.0, istrng=150.0, radiopt=0,
maxitn=1000, fillratio=1.5,
/
Residues considered as REC
RRES 1 468
END
Residues considered as LIG
LRES 469 683
END
Residues to print
RES 1 683
END
END
>>>
If I don't include the &decomp section in the original input file, then
the -make-mdins flag produces two input files *mdin and *mdin2 and but this
time respects the memopt flag.
Should one assume that per-residue decomposition is not implemented yet
with memopt=1,2,3 and for membrane proteins?
If it is, can I add the &pb section parameters I need for membrane proteins
back into the three mdin files (complex, receptor, ligand)?
Also, will the three mdin files (complex, receptor, ligand) files be all I
would need to change?
Thanks,
Ravi
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Received on Fri Feb 18 2022 - 20:30:02 PST
