Re: File format convert

From: Andreas Svrcek-Seiler <>
Date: Thu 20 Dec 2001 13:58:53 +0100 (CET)

> 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 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
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
3b) use xyzedit to create a periodic box from your single
3c) do some minimzation/MD with the H2Os in the empty box to get 'better
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
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

I hope it helps,
good luck

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Thu Dec 20 2001 - 04:58:53 PST
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