VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Sun Feb 07 2010 - 11:51:03 CST

Dear all,

I am trying to generate a psf file for a two layer molecule which consists of four guanine molecules in each layer. There is also a sodium ion between the layers. If I use the pdb file which is using MOL after the name of each atom and use AutoPSf to generate the psf file, I come up with the message"Autopsf has detected 1 unparametrized component" with the (1:MOL 4atoms)in a box specifying the atom. If I use the GUA instead of MOL as I am dealing with guanine molecules it tells me that the psf file has been completed but, neither VMD nor Rasmol could open the file. Also the total number of 129 atoms in the original pdb file reduces to 33 atoms in autopsf file. I tried different names for sodium atom(GUA, HETATM and even without the sodium atom) but, all give me the same result. I have also used a different DNA pdb file directly from pdb.org(pdb ID=325d) to make the psf file but, I see the error"autopsf has detected 88 unparametrized components". I am just wondering whether anyone has any experience in this case or not. I have attached the guanine pdb file with the name of MOL for all atoms.

Thanks a lot

Parisa