Dear AMBER Users,
I am trying to simulate a membrane protein using implicit solvent model.
Using amber14 manual, I prepared the minimization file (min.in) however i
failed in this step.
The prmtop and inpcrd files are generated using tleap and i didn't solvate
the box and the files does not contain peroidic boundary information.
However, in min.in file I used options membraneopt=1, peroidic boundary
conditions (bcopt=10) as there is a option to simulate with boundary
conditions (as mentioned in amber14 manual page 77).
The min.in file input commands are shown below
minimize structure
&cntrl
/
&pb
/
imin=1,
maxcyc=1000,
membraneopt=1,
solvopt=1,
bcopt=10,
eneopt=1,
sasopt=2,
epsmemb=1.0,
cut=999.0,
rgbmax=999.0,
igb=8,
saltcon=0.15,
phiout=1,
phiform=1,
intdiel=1.0,
extdiel=78.5,
ntpr=100,
ntx=100,
ntr=1,
restraintmask'.CA,C,O,N',
restraint_wt=5.0
/
However, running the sander command shows error as " no box info found in
inpcrd file".
Kindly advice how to include box information for implicit solvent models in
prmtop and inpcrd files.
Also, I would like to know is there any amber tutorial for implicit
membrane protein simulation.
Thank You,
Balaji
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Received on Mon Apr 11 2016 - 11:00:03 PDT
