Hi, members and developers!
Make it easy:
I am doing SMD with amber14 in following code:
namelist...
.....
jar=1,
/
&wt type='DUMPFREQ' ,istep1=2000, /
&wt type='END', /
DISANG=rst.RST
DUMPAVE=dis_VS_t
LISTIN=POUT
LISTOUR=POUT
-------------------------------------------
rst.RST file:
&rst
iat=-1,-1,
r2=5.5,r2a=20,rk2=100,
igr1=1978,1979,1990,1991, (conserved atoms in protein)
igr2=3593,3594,3595,3596,3597,3598,3599,3600,3601,3602,3603,3604 (my ligand)
&end
which steered the center of mass of igr1 and igr2 from 5.5 to 20.
But I find such steered path is not linear. My ligand didn't be pulled OUT from the pocket, but only #####walk on the surface of protein######. I mean that the ligand is still on the surface of protein although the reaction coordinate I defined increase. I want the ligand get out of protein completely, and how Amber can do that? ( and I don't think the LCOD type would help me but I'm not surewhether Iam correctly)
Hope you can understand what I point out and appreciate for your replies!!!
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Received on Fri Jan 09 2015 - 06:30:03 PST
