AMBER Archive (2002)

Subject: regarding resp-doubts

From: thenmalar rathinavelan (thenmalrr_at_yahoo.co.in)
Date: Thu Oct 03 2002 - 03:21:51 CDT

Dear Amber users,

I have a few doubts regarding the example given in
directory amber6/examples/resp_charge_fit/adenine

They are:

(i) It seems that number of atoms for adenine is
lesser than the usual situation (given-26). It
will be very nice if the pdb file is provided for
that.
 
(ii) in ade_1st.in file, I am not able to understand
the line below:

  1 16 1 17 1 18 1 19 1 20 1
 23 1 24 1 25
  1 26 2 20 2 24 2 25 2 26
 
I like to know why particularly atom numbers
16,17,18,19,20,23,24,25,26 of mol1 & 20,24,25,26
of mol2 alone is choosen for the constraint.

(iii) in ade_2st.in file the following constraints are
given:
         6 0
         1 22
  These constraints corresponds to which carbon and
hydrogen atom? & what is the basis for choosing
ivary as 0 & 22 for this two atoms alone. In the same
input itself all the other ivary is choosen to be -1,
while it is 0 in stage 1 fitting.

I am very much thanful to those who can clarify my
doubts.

Thenmalar

________________________________________________________________________
Missed your favourite TV serial last night? Try the new, Yahoo! TV.
       visit http://in.tv.yahoo.com