Hi everybody,
I'm a complete novice in this and I'm trying to follow the Manual.
In summary, I'm trying to identify receptor tunnel(s) through which a ligand can be released from the binding pocket.
I'm using the restraint and input files attached at the end of this message.
As can be seen from the .rst file, I'm changing the restraint between atoms. I have a feeling that this is wrong. Wouldn't it be better to use something like a distant restraint between the centre of mass of the protein and the ligand? If so, how can one define these centres? In this case, I assume that the iat variable would have to be changed. To what?
A second question relates to the directionality of the "push"? Is there one? Should one repeat the simulation using different atoms within the binding pocket of the protein?
Apologies if these questions are naive but I need to start from somewhere and I'm not at all familiar with restraints applied in NMR.
Thanks in advance for any help
George
======================
dist.RST
# Change distance restraint between atoms
&rst iat=1533,2223, r2=4.492, rk2=14.0, r2a=18.0 / #1533 (protein atom); 2223 (ligand atom)
smd.in
smd 2wc6-bombykol
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1, ntwx=1, ntwr=1,
ntt=3, gamma_ln=2.0, ig=-1,
temp0=300.0,
jar=1,
/
&wt TYPE='DUMPFREQ', istep1=1, /
&wt TYPE='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
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Received on Tue Jan 24 2012 - 06:00:03 PST
