AMBER Archive (2002)

Subject: questions about resp

From: X. Tan (xjtan_at_u.washington.edu)
Date: Tue Jan 08 2002 - 10:31:55 CST

Dear amber user,

Now I am working on RESP. I'd like to fit the charges of
two or three conformations. So I refer to the example of RESP/bis-napthyl.
But there are something in that example I am not very clear. 1. in the
bis_1.in file, it shows that the charge of napthyl is -99. Here does this
"-99" mean charge frozen at initial charge values.
 .....
 napthyl 1-
  -99 29
    6 0
    6 0
 ....
 2. what is the exact meaning of the following part.
 ....
   13 -1.000
    1 19 1 20 1 21 1 22 1 23 1 24 1 25 1 26 1 27 2 20 2 25 2 26 2 27
 ....

and the part,
....
    2
    1 1 2 1
    2
    1 2 2 2
    2
    1 3 2 3
    2
    1 4 2 4
    2
    1 5 2 5
 .....
3. in the bis_2.in file, many atoms' ivary were assigned
a value "-1", what does that mean? .... napthyl 1-
  -99 29
    6 -1
    6 -1
    6 -1
    6 -1
 ....
 4. For the esp.dat file, what I need do is just combine the
several esp.dat for each confamation into one file. Is that right?
 Thanks for your kind help.

 Xiaojian Tan