Hi.
Have you think to use the centre of mass of the protein instead? (or all
the CA of the protein if it's easy) That way the ligand will be getting
separated from the protein, instead of moving over the surface.
Other alternative is going farther away with the distance, instead of
stopping at 20 move it to 40 or 50 and see if it moves away from the
surface.
2015-01-09 14:59 GMT+01:00 Chris <dlutlife223.163.com>:
> 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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>
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Received on Sun Jan 11 2015 - 05:00:03 PST
