Hello all,
I want to perform a MM-PBSA calculation for a membrane-protein system using the following input. How do I estimate the mctrdz and mthick from the MD trajectory? Can this be done using cpptraj or do I need an external program? Any help would be appreciated.
&general
use_sander=1,
startframe=1, endframe=3000, interval=10,
keep_files=2, debug_printlevel=2
/
&pb
radiopt=0,
indi=20.0,
istrng=0.150,
fillratio=1.25,
ipb=1,
nfocus=1,
bcopt=10,
eneopt=1,
cutfd=7.0,
cutnb=99.0,
npbverb=1,
solvopt=2,
inp=1,
memopt=1,
emem=7.0,
mctrdz=0.0,
mthick=36.086,
poretype=1,
maxarcdot=15000
/
Thanks and best regards,
—
Sinjini Bhattacharjee
PhD Student
Molecular Theory and Spectroscopy
Max-Planck-Institut für Kohlenforschung
45470 Mülheim an der Ruhr, Germany
email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
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Received on Wed Mar 20 2024 - 06:00:02 PDT
