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

[Axel Kohlmeyer]

On Tue, 3 Apr 2007, Yuming Sun wrote:

YS> Dear All,

dear yuming sun,

YS>   to do QM/MM simulation using CPMD, i have spent a week to generate

first of all, please tell us _which_ QM/MM interface you
are planning to use (and which force field). there is more
than one option...

YS> the molecular topology and cartesian coordinates from the PDB file.

before even considering to start a QM/MM run, you should 
make sure that your system is equilibrated well classically.
With the gromos based QM/MM interface, that means you have
to set up and run your system with either gromos or amber.
so the question is more of how you set up a run with those
packages and not cpmd, so you may want to check the corresponding
mailing lists etc. in the case of gromos, you'll automatically
have a working topology, in the case of amber, you'll have to
use (a recent version!) of the amber2gromos package.

with the gromacs based interface, you'll be essentially running 
a gromacs run that'll start cpmd to run single point calculations,
so again, you'll have to figure out how to set up your system
with gromacs.

generally, i _strongly_ recommend to practice running QM/MM
with a small test system (10-alanin helix or similar) before
trying to set up a more complicated system.

YS> I found that the PRODRG server can only produce coordinates in
YS> gromos87 format without topology file in gromos format, the pdb2gmx
YS> program in GROMACS-3.3.1 can produce the coordiantes in gromos96
YS> format, but i am wondering the topology file generated by pdb2gmx
YS> can be directly used by CPMD. If can't, how can i generate the
YS> proper topology file, because i did not find the way in gromos96.

as far as i know, pdb2gmx creates gromacs topologies, which are
quite different from gromos.

so please provide more details on what you really intend to do
and perhaps check with more appropriate forums with respect to
how to set up the classical runs first.

cheers,
   axel.


YS>   Thanks
YS>    
YS> 
YS> 
YS> Dr. Yuming Sun
YS> Department of Physics
YS> Yantai University
YS> Yantai, Shandong 264005
YS> P.R. China
YS> Tel. 86-535-6904965
YS> Fax  86-535-6901947
YS>  		
YS> ---------------------------------
YS>  ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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