AMBER Archive (2005)

Subject: AMBER: parameters in gaff.dat

From: Lihua Wang (lhw_at_broyde.nyu.edu)
Date: Fri Apr 15 2005 - 00:21:29 CDT

Hi all,

i am trying to pick from gaff.dat possible parameters for use with a
modified nucleotide.

I would like to know the following:

1. What is the purpose of having two atom types that are identical? for
example, cd is supposed to be identical to cc. Then why is it necessary
(or advantageous) to have two names for one type?

2. If two atom types are 'identical' as indicated in gaff.dat, can i
suppose that they are interchangeable? if they are truly identical, why
are some parameters that are supposed to be 'identical' vastly different?
For example:

nd-cc-nh are nc-cd-nh are 72.4 120.11 while
nc-cc-hn and nd-cd-nh are 73.9 111.94

since nd is identical to nc and cd is identical to cc, shouldn't the four
parameters be all the same? why the parameters are different, especially
for the angle itself (120.11 vs. 111.94 sounds like sp2 vs. sp3
hybridization)? Am I missing or misunderstanding something?

I noticed there is a similar question on the mail list archive but it is
not answered.
http://amber.ch.ic.ac.uk/archive/200411/0027.html

Thanks in advance for your help.

Lihua
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