From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Thu Sep 25 2008 - 16:18:40 CDT
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
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