Hi,
> Regarding the scaling constant (which "preventively" scale restraints)
> when SC pot. are used: 1/lambda versus 1/(1-lambda) maybe it is not
> the "full typo" as this is probably dependent on simulated process. For
> the ligand "disappearing" scaling constant
> is 1/(1-lambda) for the opposite process (appearing) perhaps 1/lambda is
> used. This would correspond to the disappearing/appearing
> SF-potentials where in case of disappearing multiplicative constant
> (1-lambda) is used and in case of appearing it is just lambda.
True, maybe that was my idea when writing it. However, I think only the
setup in which whole restrained ligands disappear has ever been used.
> #1 - appearing of the restraints while ligand is fully (vdw/el)
> interacting with receptor during this process
>
> Here I would use this approach:
>
> V0 = Receptor + Ligand (in water)
> no restraint is applied in V0 ( ifsc=0, scmask='',crgmask='' )
> dvdl_norest=0
>
>
> V1 = Receptor + Ligand (in water)
> Ligand is restrained in V1 with target restraints (defined in the RST
> file) (ifsc=0, scmask='',crgmask='')
> dvdl_norest=0
yes, that is how I would do it. This linearly increases the restraint
strength with lambda, which is what you want.
> #2 Decoupling (vdw/el) the fully restrained ligand.
>
> Here I would use this setup:
>
> V0 = Receptor + Ligand (in water)
> Ligand is restrained in V0 with target restraints (defined in the RST
> file) (ifsc=1, scmask=':LIGAND',crgmask='')
> dvdl_norest=1
>
>
> V1 = just Receptor (in water)
> ( ifsc=1, scmask='',crgmask='' )
> dvdl_norest=1
>
that is also right, but I think dvdl_norest can be left out in V1, it has
no real effect there. It is necessary in V0. In this setup, the ligand
will decouple, but will still be restrained with unchanged strength.
> Anyway the second possibility for V1 might be here:
>
> V1 = Receptor + Ligand (in water) where all the ligand atoms are DUMMY
> atoms.
> Ligand is restrained in V1 with target restraints (defined in the RST
> file) (ifsc=1, scmask=':LIGAND' or scmask='' ???, crgmask='')
> dvdl_norest=1
>
No, that is not useful. Dummy atoms and softcore are mutually exclusive
ways to do the same thing and they cannot be mixed like this. Stick to the
first way you suggested.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed May 09 2012 - 08:30:02 PDT
