AMBER Archive (2002)

Subject: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Fri Nov 01 2002 - 03:08:20 CST

Dear all,

Two questions:

question 1) I am using LEAP from AMBER7 to obtain the topology file of
ibuprofen
(as example).
I created a prep input file with a tree ordering M, E, S, B( file:
ligand_prp_resp.in)

After executing TLEAP as follow:
tleap
source leapibu.in

I obtain the topology file (file: ibu.top) but with different tree
symbols (ITREE) that correspond to the flag TREE_CHAIN_CLASSIFICATION in
the topology file.

Why does LEAP change the topological type of some atoms?
I would like to conserve the topological type in the prep file.

For example the topological type for C5 is M in the prep file and is B
in the topology file.
C12 is M in the prep file and S in the topology file.

I send you the input files.

question 2) there are no parameters for c-ct-ca or c2-ct-ca in the gaff
force
field.

Thanks
pascal

ibu.top (just a piece)

%FLAG
AMBER_ATOM_TYPE
%FORMAT(20a4)
o c oh ho c3 hc c3 hc hc hc ca ca ha ca ha ca c3 hc
hc c3
hc c3 hc hc hc c3 hc hc hc ca ha ca ha
%FLAG
TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M S E M E 3 E E E M B E B E B 3 E
E 3
E 3 E E E 3 E E E S E M E

ligand_prep_resp.in

    0 0 2

This is a remark line
molecule.res
MOL XYZ 0
CHANGE OMIT DU BEG
 0.0000
 1 DUMM DU M 8.000000 1.500000 2.000000 0.000000
 2 DUMM DU M 8.000000 1.500000 0.500000 0.000000
 3 DUMM DU M 7.000000 1.500000 0.500000 0.000000
 4 O1 o M -3.362 -1.367 -0.952 -0.529
 5 C2 c M -3.647 -0.486 -0.164 0.610
 6 O2 oh S -4.958 -0.285 0.261 -0.635
 7 H5 ho E -5.483 -0.977 -0.215 0.440
 8 C1 c3 M -2.692 0.545 0.496 0.162
 9 H1 hc E -2.935 0.551 1.558 0.019
10 C3 c3 3 -2.987 1.961 -0.066 -0.114
11 H2 hc E -2.372 2.697 0.443 0.039
12 H3 hc E -4.032 2.213 0.090 0.039
13 H4 hc E -2.773 2.010 -1.129 0.039
14 C4 ca M -1.221 0.144 0.330 -0.001
15 C5 ca M -0.651 -0.013 -0.930 -0.210
16 H6 ha E -1.252 0.136 -1.817 0.147
17 C6 ca M 0.681 -0.368 -1.064 -0.130
18 H7 ha E 1.100 -0.490 -2.054 0.130
19 C7 ca M 1.485 -0.573 0.053 0.005
20 C8 c3 3 2.959 -0.958 -0.090 -0.089
21 H8 hc E 3.180 -1.776 0.593 0.036
22 H9 hc E 3.142 -1.320 -1.099 0.036
23 C9 c3 3 3.939 0.212 0.215 0.308
24 H10 hc E 3.715 0.587 1.214 -0.041
25 C11 c3 3 3.768 1.378 -0.785 -0.281
26 H14 hc E 4.448 2.188 -0.541 0.061
27 H15 hc E 2.754 1.764 -0.758 0.061
28 H16 hc E 3.981 1.049 -1.798 0.061
29 C10 c3 3 5.398 -0.299 0.211 -0.281
30 H11 hc E 6.084 0.507 0.453 0.061
31 H12 hc E 5.664 -0.692 -0.765 0.061
32 H13 hc E 5.529 -1.090 0.944 0.061
33 C12 ca M 0.912 -0.416 1.311 -0.130
34 H17 ha E 1.513 -0.576 2.197 0.130
35 C13 ca M -0.420 -0.064 1.447 -0.210
36 H18 ha E -0.842 0.050 2.437 0.147

LOOP
C4 C13

IMPROPER
C1 O1 C2 O2
C1 C13 C4 C5
C4 C12 C13 H18
C13 C7 C12 H17
C4 C6 C5 H6
C5 C7 C6 H7
C8 C12 C7 C6

DONE
STOP 

--

***************************************************
 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
 Manchester, M13 9PL, U.K
 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3