AMBER Archive (2003)

Subject: charge fitting for c-term homocysteine.

From: X. Tan (xjtan_at_u.washington.edu)
Date: Thu May 22 2003 - 21:25:19 CDT

Dear amber users,

I want to calculate the charge for a c-term homocysteine. Basically I
follow the procedure in the paper of Piotr Cieplak et al(JCC. 1995). I
have two conformations for homocysteine, alpha-helix form and beta-sheet
form. I can get the decent charges for central form homocysteine. Also the
charges look fine if I fit either alpha-helix form or beta-sheet form
homocysteine with the acetate. The problem is if I try to fit both
conformations with acetate, it gave weird charges(1.3 for C(o2), and
-1.00 for O(co2). I can not figure out what's going on
with my RESP calcualtion. Is there anyone can help me? I attached my input
file as below.

------------------------------------------------------
resp for homocys_block_1
 &cntrl
   nmol=3, ihfree=1, iqopt=1,
 &end
1.0
homocys_block_a
    0 26
    6 0
    1 0
    6 0
    8 0
    1 0
    1 0
    7 0
    6 0
    6 0
    8 0
    6 0
    6 0
   16 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    7 0
    6 0
    1 0
    1 0
    1 0
    1 0
    6 0.00000
    1 1 1 2 1 3 1 4 1 5 1 6
   20 0.00000
    1 7 1 8 1 9 1 10 1 11 1 12 1 13
1 14 1 15 1 16 1 17 1 18 1 19 1 20 1 21
    1 22 1 23 1 24 1 25 1 26

1.0
homocys_block_b
    0 26
    6 0
    1 0
    6 0
    8 0
    1 0
    1 0
    7 0
    6 0
    6 0
    8 0
    6 0
    6 0
   16 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    7 0
    6 0
    1 0
    1 0
    1 0
    1 0
    6 0.00000
    2 1 2 2 2 3 2 4 2 5 2 6
   20 0.00000
    2 7 2 8 2 9 2 10 2 11 2 12 2 13
    2 14 2 15 2 16 2 17 2 18 2 19 2 20
    2 21 2 22 2 23 2 24 2 25 2 26

1.0
ch3coo-
   -1 7
    6 0
    1 0
    1 0
    1 0
    6 0
    8 0
    8 6

   12 0.00000
    1 21 1 22 1 23 1 24 1 25 1 26
1 9 1 10 3 1 3 2 3 3 3 4
   12 0.00000
    2 21 2 22 2 23 2 24 2 25 2 26 2 9
2 10
    3 1 3 2 3 3 3 4

    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
    2
    1 6 2 6
    2
    1 7 2 7
    3
    1 8 2 8 3 1
    2
    1 9 2 9
    2
    1 10 2 10
    2
    1 11 2 11
    2
    1 12 2 12
    2
    1 13 2 13
    2
    1 14 2 14
    2
    1 15 2 15
    2
    1 16 2 16
    2
    1 17 2 17
    2
    1 18 2 18
    2
    1 19 2 19
    2
    1 20 2 20
    2
    1 21 2 21
    2
    1 22 2 22
    2
    1 23 2 23
    2
    1 24 2 24
    2
    1 25 2 25
    2
    1 26 2 26

-----------------------------------------------
Sorry. The format for the group constraint part have been messed up
bacause the email process. I used the 16I5 format.

Thanks for any suggestions!

Xiaojian Tan