Dear AMBER,
Recently, I'm calculating the binding energy of membrane protein by pbsa (amber16) with implicit membrane model.
There I am getting the following the message:
"Cannot match namelist object name mprob
namelist read: misplaced = sign
Cannot match namelist object name .7"
The code in the file that pbsa is trying to read is:
&cntrl
ntx=1, imin=1, ipb=1, inp=0
/
&pb
npbverb=0, epsout=80, epsin=1, epsmemb=4, radiopt=0,
dprob=1.4, sasopt=0, membraneopt=1, mthick=32.0,
space=0.5, fillratio=2, nfocus=1, solvopt=1,
accept=1e-4, maxitn=1000, mprob=2.70,
bcopt=10, eneopt=1, cutnb=10, cutfd=7.0,
/
When I remove this parameter(mprob=2.70), there is no such information. But the two result calculated is the same.
the final result in out.file is:
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -82722.3621 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -7368.7223
EELEC = -75353.6398 EPB = 0.0000 RESTRAINT = 0.0000
ECAVITY= 0.0000 EDISPER = 0.0000
According to the manual, the MPROB is Membrane probe radius (default 2.70 Å), which is used to specify the highly different lipid molecule accessibility versus that of the water. So I wonder if I can ignore this message because of the same results. If not, what should I do?
Thank you in advance.
Zhenmei Gao
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Received on Mon Sep 17 2018 - 07:30:02 PDT
