Hi,
> The outputs of tleap ,prmtop,prmcrd are very usefull for
> amber pakages.
> But,I want to use these parameteres to Tinker program.
> But it is difficult for me to recreate molcules or force field
> for tinker.so I thought somebody may be created the
> converter.I hear that babel is good, but babel does
> not covert prmtop,prmcrd to xyz file.
According to my (limited) experience, the easiest way to do the conversion
is:
1) create a pdb file from prmtop and prmcrd (using pdbgen)
2) apply the pdbxyz program to this pdb file (some additional minor tweaks
to the pdb file might be necessary to get a xyz file).
if (!expicit_solvent) done;
3) if you want explicit solvent and amber parameters,
3a) create a xyz-file with one TIP3P water
(tinker does not add the H-H 'bonds' to the waters, I don't know if that
hurts)
3b) use xyzedit to create a periodic box from your single TIP3P.xyz
3c) do some minimzation/MD with the H2Os in the empty box to get 'better
water'
3d) use xyzedit to soak your solute in the box
3e) perform the usual steps to get a goot starting conformation
3f) start MD an see if all work out as expected.....
... all this comes from 'playing around', there might be easier
solutions.
the ewald implementation in tinker *seems* slow, but I don't have AMBER6,
so I can't compare. besides, I know little about the internals of the
ewald method, so I might have overlooked some ways to accelerate the
calculations.
I hope it helps,
good luck
andreas
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Received on Thu Dec 20 2001 - 04:58:53 PST
