Subject: Tinker: atom type format for OPLSAA or AMBER

From: Per Tetzschner Olsen <[email-masked]>
Date: Thu, 18 Apr 2002 11:52:11 +0200

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).

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)

regards

Per Tetzschner

University of Southern Denmark
[email-masked]
+45-65502570

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From: "Nicolas Ferre'" <[email-masked]>
Date: Thu, 18 Apr 2002 12:39:58 +0200

Hi,

In principle, Molden should be used for your purpose (i.e. Tinker's
Amber, MM3 and Charmm forcefields), but unfortunatly the actual
conversion (pdb -> FF) does not match the last version of Tinker
parameters (version 3.9).
Let's hope it will be corrected soon (this is a request to G.
Schaftenaar, Molden's author), or you can correct the Molden source
yourself ...

Nicolas

Per Tetzschner Olsen wrote:
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nicolas FERRE' (PhD)
				 phone/fax : +39-0577-234278
Dipartimento di Chimica
Universita` di Siena             mailto:[email-masked]
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From: John Shelley <[email-masked]>
Date: Thu, 18 Apr 2002 09:22:30 -0700 (PDT)

Dear Per,

    Sorry if I misunderstand your query.

> of calculate the 'not diagonalized' Hessian).

MacroModel should be able to calculate the analytical gradient (from the
command line).

If you take the .com file from an energy listing run and include the
command:

 DLST    1

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.

> University of Southern Denmark

Hope this helps.  If not you might try writing to [email-masked].

John Shelley
Senior Scientist
Schrodinger, Inc.