psf generation for a small non-peptide molecule

From: CHINDEA Vlad (
Date: Thu Sep 25 2008 - 16:18:40 CDT

Hello everybody

As I am new to the NAMD program I have run into problems with psf generation.

As top_all27_prot_lipid topology file supplied with NAMD tutorials is specificaly made for proteins and lipids I am not sure I am using correct atom types for my molecule.
Chemically-wise this molecules contains Sp3 carbons, polar and nonpolar hydrogens, hydroxyl, ester and ether oxygens, tertiary amine nitrogens. Particullary I am not sure what are the proper atom types for ether oxygen and tertiary amine nitrogen in this topology file. Do you have any suggestions ?

Further more is there any other, more general maybe, topology file that should be more suitable for this kind of modelling tasks ?

Many thanks and kind regards

Vlad Chindea
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