Tinker: atom type format for OPLSAA or AMBER
- From: Per Tetzschner Olsen <tetz.,at,.thor.chem.sdu.dk>
- Subject: Tinker: atom type format for OPLSAA or AMBER
- Date: Thu, 18 Apr 2002 11:52:11 +0200
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)
University of Southern Denmark