RE: PSF file generation

From: JC Gumbart (
Date: Tue Aug 16 2005 - 01:00:32 CDT

I'm not confident I understand your specific problem but I would suggest
using psfgen to create all psf (and pdb) files to be used for simulations
instead of writing them by hand. You will need to create a topology file if
you have not done so already to define the specific connectivity in your

-----Original Message-----
From: [] On Behalf
Of Tamal Banerjee
Sent: Tuesday, August 16, 2005 12:17 AM
Subject: namd-l: PSF file generation

I have made the psf ,pdb and parameter file for a new compound and also
done the minimization routine to it.It all works fine.
But when i want to make the PBC condition.I created the pdb file for 10
molecules (to start with)but somehow the error message shows that no of
atoms in psf and pdb file should be same.
Is it true that i have to enter the connectivity of all the molecules
within the psf file.Since the molecule is same i numbered the atom by
giving different segment names to each molecule keeping the numbering
within the molecule same.
Please advise me how i should write the psf and pdb file and also the
parameter file for such 'n' no of molecules.



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