Subject: MD simulation of proteins with TINKER

From: [email-masked] (Peter Happersberger)
Date: Sat, 28 Feb 1998 11:55:11 +0100

Dear CClers

  I would like to do some MD simulations of solvated proteins (e.g. BPTI)
with the program package TINKER V3.5 (http://dasher.wustl.edu/tinker/)
under Linux.
But till now, I couldn't generate a TINKER specific start file (*.xyz).

What I have done:

1. I have generated a solvent volume around the protein BPTI (pdb1bpi.ent)
   with the program SOLVATE
   (http://www.imo.physik.uni-muenchen.de/~grubi/solvate/docu.html).

2. After conversion of the pdb-file to the tinker specific xyz-file
   (TINKER program 'pdbxyz') I have started the MD simulation with the
   TINKER program 'dynamic'.
   The program stopped after a short time with several error messages,
   such like

 Enter Potential Parameter File Name :  amber

 Undefined or Illegal Atom Types :

 Type          Atom Number     Atom Type

 Atom                1              0
 Atom .......
 ............
 Atom              446              0
 Atom              447              0

 Atoms with an Unusual Number of Attached Atoms :

 Type           Atom Name      Atom Type       Expected    Found

 Valence           1-OH2            0              0         2
 Valence           2-H1             0              0         1
 ...................
 Valence         447-H2             0              0         1

 MECHANIC  --  Some Required Potential Energy Parameters are Undefined

 TINKER is Terminating due to the Occurrence of a Severe Error

By contrast, the MD simulation without the water shell (e.g. only
the protein) succeded.

I am appreciated greatly if any one give me some information how I can
generate a "correct" xyz-file.
Could anybody send me a "correct" example files
(xyz-, seq-, pdb-, key-, ...) which are neccessary to start a MD
simulation?

Thank you,
Peter Happersberger

-- 
------------------------------------------------------------------------
Peter Happersberger
Ph.D. Student
Faculty of Chemistry
University of Konstanz
Email: [email-masked]
URL: http://sg17.chemie.uni-konstanz.de/~peha/
Voicenet: ++49-(0)7531-88-3928 or Fax: ++49-(0)7531-88-3097
Papernet: AG Przybylski, P.O. Box M 732, 78457 Konstanz, Germany
-------------------------------------------------------------------------