[CPMD-list] =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=20How=20to=20generate?= =?gb2312?q?=20the=20molecular=20topology=20and=20cartesian=20coordinates=20?= =?gb2312?q?from=20PDB=20file?=

[Axel Kohlmeyer]

On Tue, 3 Apr 2007, Yuming Sun wrote:

YS> Thanks to Axel. There may be some confusion in my last e-mail. I am
YS> to do QM/MM with Gromos96, the pdb2gmx is used just to produce the
YS> needed coordinate file in Gromos96 format, but I don't know how to
YS> produce the topology file in Gromos96 format.

well, that depends on what force field you intend to use.
in case of gromos, you - of course - need to use 
gromos to set up _and_ equilibrate your system and then
you get the matching topology 'for free'.

in case of amber you have to use amber to generate 
the amber 'parm'-file (=topology) and 'crd'-file 
(=coordinates) and then use amber2gromos to convert 
them to gromos format. again, classical equilibration
is _essential_ and so your problem is not really a
cpmd problem.

in case you want to do something else, you have to
write the topology manually. which is not too difficult,
but needs some studying of the gromos manuals (and
topology writing/reading code).

still, for as long as you don't tell us what kind
of a system you are actually thinking about, we 
cannot help you.

cheers,
   axel.

YS>    
YS>   Thanks
YS> 
YS> Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> дµÀ£º
YS>   

-- 
=======================================================================
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
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.