[CPMD-list] Tool for CPMD-input creation

[Ari P Seitsonen]

Dear Rad Balu,

  Well, your system is going to require a _LOT_ of computer resources, but
provided you have access to them...

  I don't know of any direct way of transforming the PDB file to CPMD 
input, but the first guess would be to use the keyword "ANGSTROM", give 
the cell vectors from the PDB file manually using "CELL VECTORS" and 
transforming the PDB file first to an XYZ file and then ordering the 
atoms according to the species:

# babel coords.pdb coords.xyz
# tail +3 coords.xyz | sort | awk '{ print $2, $3, $4, $1 }' > coords.txt

Then copy these to your input file and add the section on the pseudo and 
number of atoms in front of each species (well, with a small effort you 
can get 'awk' etc to count the atoms per species for you).

  After this you need to specify all the rest for CPMD, like the cut-off 
energy etc.

    Greetings,

       apsi

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 Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
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On Tue, 27 Apr 2004, Rad Balu wrote:

> Hi All,
> 
> Is there any tool to create input for the CPMD program. I am planning to use  
> CPMD for getting the optimzed geometry for a protein(roughly 5000 atoms) in 
> PDB format. I would like to know if there is an easy way  to create the input 
> for CPMD from PDB.
> 
> Thanks
> 
> Rad Balu
> Graduate Student in Computational Chemistry
> 
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