[CPMD-list] How to generate the molecular topology and cartesian coordinates from PDB file

[Yuming Sun]

Dear All,
   
  to do QM/MM simulation using CPMD, i have spent a week to generate the molecular topology and cartesian coordinates from the PDB file. I found that the PRODRG server can only produce coordinates in gromos87 format without topology file in gromos format, the pdb2gmx program in GROMACS-3.3.1 can produce the coordiantes in gromos96 format, but i am wondering the topology file generated by pdb2gmx can be directly used by CPMD. If can't, how can i generate the proper topology file, because i did not find the way in gromos96.
   
  Thanks
   


Dr. Yuming Sun
Department of Physics
Yantai University
Yantai, Shandong 264005
P.R. China
Tel. 86-535-6904965
Fax  86-535-6901947
 		
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