[gmx-users] A strange phenomenon in the new version opls-aa force field
PeiQuan Chen
gromacs at 163.com
Fri Oct 10 02:29:00 CEST 2003
Dear gmx-users：
I have noted that a strange phenomenon in the new version opls-aa force field, which Erik Lindahl updated
on the August 06, 2003. The changes of new version parameters are minor, but involve using 4.184 instead of
4.1868 for converting between kcal and kJ, and changing the atom order for some improper torsions.
I have noted the changes of the atom order for some improper torsions can affect the topol files generated
by the pdb2gmx program. Comparing the new version and old one of the force field files, I have noted that
in the ffoplsaa.rtp file, Erik have correct the atom order for the improper torsions. But when I use the
pdb2gmx to generate topol files, the change on the improper torsions can affect the topol of normal torsions
section. The new version files generated less torsion numbers than the old one. I think that torsion section
in the old version are correct and the old one is not.
From the example, I note the torsion(1 5 7 10) exists in the old version but not exists in the
new version.
Can anybody explain this strange phenomenon for me?
For Example:
1. The *.gro files of the PHE
Good gRace! Old Maple Actually Chews Slate
23
1PHE N 1 5.511 7.702 15.527
1PHE H1 2 5.534 7.607 15.506
1PHE H2 3 5.428 7.704 15.582
1PHE H3 4 5.497 7.752 15.442
1PHE CA 5 5.622 7.763 15.603
1PHE HA 6 5.626 7.707 15.685
1PHE CB 7 5.753 7.760 15.524
1PHE HB1 8 5.738 7.799 15.434
1PHE HB2 9 5.822 7.814 15.573
1PHE CG 10 5.810 7.623 15.504
1PHE CD1 11 5.908 7.601 15.408
1PHE HD1 12 5.939 7.678 15.351
1PHE CD2 13 5.769 7.516 15.582
1PHE HD2 14 5.699 7.529 15.652
1PHE CE1 15 5.964 7.475 15.389
1PHE HE1 16 6.034 7.462 15.320
1PHE CE2 17 5.825 7.389 15.564
1PHE HE2 18 5.794 7.312 15.621
1PHE CZ 19 5.922 7.369 15.467
1PHE HZ 20 5.962 7.278 15.454
1PHE C 21 5.594 7.909 15.639
1PHE O1 22 5.476 7.961 15.599
1PHE O2 23 5.691 7.974 15.710
0.60640 0.69575 0.39018
2. The torsion section in the *.top files generated by pdb2gmx(new opls-aa version)
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 21 3
3 1 5 6 3
3 1 5 7 3
3 1 5 21 3
4 1 5 6 3
4 1 5 7 3
4 1 5 21 3
1 5 7 8 3
1 5 7 9 3
1 5 7 10 3
6 5 7 8 3
6 5 7 9 3
6 5 7 10 3
21 5 7 8 3
21 5 7 9 3
21 5 7 10 3
1 5 21 22 3
1 5 21 23 3
6 5 21 22 3
6 5 21 23 3
7 5 21 22 3
7 5 21 23 3
5 7 10 11 3
5 7 10 13 3
8 7 10 11 3
8 7 10 13 3
9 7 10 11 3
9 7 10 13 3
7 10 11 12 3
7 10 11 15 3
13 10 11 12 3
13 10 11 15 3
7 10 13 14 3
7 10 13 17 3
11 10 13 14 3
11 10 13 17 3
10 11 15 16 3
10 11 15 19 3
12 11 15 16 3
12 11 15 19 3
10 13 17 18 3
10 13 17 19 3
14 13 17 18 3
14 13 17 19 3
11 15 19 17 3
11 15 19 20 3
16 15 19 17 3
16 15 19 20 3
13 17 19 15 3
13 17 19 20 3
18 17 19 15 3
18 17 19 20 3
3. The torsion section in the *.top files generated by pdb2gmx(old opls-aa version)
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 21 3
3 1 5 6 3
3 1 5 7 3
3 1 5 21 3
4 1 5 6 3
4 1 5 7 3
4 1 5 21 3
1 5 7 8 3
1 5 7 9 3
1 5 7 10 3
6 5 7 8 3
6 5 7 9 3
6 5 7 10 3
21 5 7 8 3
21 5 7 9 3
21 5 7 10 3
1 5 21 22 3
1 5 21 23 3
6 5 21 22 3
6 5 21 23 3
7 5 21 22 3
7 5 21 23 3
5 7 10 11 3
5 7 10 13 3
8 7 10 11 3
8 7 10 13 3
9 7 10 11 3
9 7 10 13 3
7 10 11 12 3
7 10 11 15 3
13 10 11 12 3
13 10 11 15 3
Sincerely yours
----
PeiQuan Chen
________________________________________________________________________
PeiQuan Chen Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone: (86)2223507510 Mobile Phone: (+86)13920675030
gromacs at 163.com
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