parameters for NAD,NAG,NAP

From: bora erdemli (
Date: Thu Feb 03 2005 - 03:39:00 CST


Basically I have two questions;

1) I am going to simulate protein complexes which have
the following hetero groups NAD,NAG and NAP. What if I
simulate only the protein complexes by extracting from
PDB file without heterogroups? Does it have an effect
which alters the physical results of my simulation?

2)If I have to do the simulation together with the
hjeterogroups, I need parameter and topology files
which include parameters for these groups. Previously,
I use param27 and topol27 files but they only contains
infromation for NAD but not the others. Does anybody
have releavent information about the parameters that I

sincerely yours


Sabri Bora Erdemli
Koc University
Computational Science and Engineering
Research and Teaching Asistant
Koc Universitesi pk.218 34550
sariyer Istanbul/TURKEY
tel no: 02123381736

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