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
Received on Fri May 23 2003 - 03:53:01 PDT
