[CPMD-list] Tool for CPMD-input creation

[Axel Kohlmeyer]

>>> "RB" == Rad Balu <radbalu at comcast.net> writes:

RB> Hi All,

hi,

RB> Is there any tool to create input for the CPMD program. I am planning to use  
RB> CPMD for getting the optimzed geometry for a protein(roughly 5000 atoms) in 
RB> PDB format. I would like to know if there is an easy way  to create the input 
RB> for CPMD from PDB.

there is not automated way, but with the use of some standard unix 
utilities it should be rather easy. first you'd have to check, if your
PDB file includes all hydrogen atoms. if not you'd have to run it
through some (classical) molecular modelling program to generate the 
coordinates. next, i'd suggest converting the pdb file to .xyz format
with the babel program, e.g. 'babel -ipdb protein.pdb -oxyz protein.xyz'.
the .xyz file only contains the atoms types and the coordinates in
angstrom.

now you'll only have to extract the coordinates for each species
separately and add them to the input file. so after adding the 
initial pseudopotential file line and the number of atoms you can use
something like:

awk '/^ *C +/ { printf "%12.5f%12.5f%12.5f\n",$2,$3,$4;}' protein.xyz >> protein.in

to add the carbon coordinates to the end of your input file.
with all other atoms times you can do it similarly.

btw.: this is a _very_ ambitious project. i hope you have secured 
enough (parallel) computer time and disk storage to handle it. 

good luck,
     axel kohlmeyer.

RB> Thanks

RB> Rad Balu
RB> Graduate Student in Computational Chemistry

RB> _______________________________________________
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RB> http://www.cpmd.org/mailman/listinfo/cpmd-list



--

=======================================================================
Axel Kohlmeyer       e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.