Re: CCL:Tinker: atom type format for OPLSAA or AMBER
- From: John Shelley <jshelley-0at0-schrodinger.com>
- Subject: Re: CCL:Tinker: atom type format for OPLSAA or AMBER
- Date: Thu, 18 Apr 2002 09:22:30 -0700 (PDT)
Sorry if I misunderstand your query.
On Thu, 18 Apr 2002, Per Tetzschner Olsen wrote:
> Hi CCL
> I am working with the TINKER package (ver. 3.9), because I am
> interested in the analytical Gradient and the 'not diagonalized'
> Hessian for different kinds of molecular systems. TINKER has
> the advantage that you can use several FF.
> Because of no Graphical interface, where you can draw your
> molecules I am using Macromodel ver. 7.0 (which is not capable
> of calculate the 'not diagonalized' Hessian).
MacroModel should be able to calculate the analytical gradient (from the
If you take the .com file from an energy listing run and include the
Then run the job from the command line (not via the interface).
The numerical and analytical first derivatives of the potential energy
should be listed in the .log file.
> My problem is when converting from Macromodel format (.dat or PDB)
> to TINKER (.xyz) with Babel or pdbxyz.x I received atomtypes
> for the molecule saying 0 (with PDBXYZ.x) or the atomtype belonging
> to MM3. What about a program which is capable of converting into
> OPLSAA, AMBER etc. ????
> I think of a program of my own, which is capable of reading:
> 1. The atom type (C,H,N.....)
> 2. The connectivity
> 3. If the atom belongs to a substructure (i.e. DNA-part)
> and convert the atom type into the approriate atom number for
> a chosen FF in TINKER.
> I would appreciate if anyone have written or know to the existence
> of such program, because manually converting of 500 atoms molecules
> takes for ever (or just really long time)
> Per Tetzschner
> University of Southern Denmark
Hope this helps. If not you might try writing to help-0at0-schrodinger.com.
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