psf generation for a small non-peptide molecule

From: CHINDEA Vlad (vchindea_at_hotmail.com)
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
_________________________________________________________________
Connect to the next generation of MSN Messenger 
http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:21 CST