Hi,
I want to build 1,4-dimethyl benzene from its fragments (i.e. a para
substituted benzene (PSB) and two methyl groups).
So I've built both fragments using g03/resp/antechamber/prepgen (see
resulting prep files below).
Now to construct methyl benzene in leap I used the following leaprc
file:
source leaprc.ff94
gaff = loadamberparams gaff.dat
loadamberprep PSB.prepin
loadamberprep CH3.prepin
mol = sequence { CH3 PSB }
saveamberparm mol methylBenzene.top methylBenzene.crd
savepdb mol methylBenzene.pdb
quit
The methyl benzene structure is incorrect. The ring is not symmetric.
However, if I build PSB or PSB-CH3 I get the correct ring structure.
I have also tried using the NOMIT keyword
in the CH3 prep file but this did not fix the problem. Since CH3-PSB
didn't work, CH3-PDB-CH3 wasn't attempted.
Has anyone got any ideas why CH3-PSB doesn't work?
Cheers,
Martin.
CH3.prepin:
0 0 2
This is a remark line
CH3
CH3 INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .
00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .
00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .
00000
4 C1 c3 M 3 2 1 1.540 111.208 180.000
-0.02133
5 H1 hc E 4 3 2 1.086 90.000 -90.000
0.00711
6 H12 hc E 4 3 2 1.085 162.350 90.000
0.00711
7 H13 hc E 4 3 2 1.086 65.459 19.517
0.00711
LOOP
IMPROPER
DONE
STOP
PSB.prepin:
0 0 2
This is a remark line
PSB
PSB INT 0
CORRECT NOMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .
00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .
00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .
00000
4 C1 ca M 3 2 1 1.540 111.208 180.000
0.13386
5 C6 ca B 4 3 2 1.384 120.000 90.000
-0.21801
6 C5 ca S 5 4 3 1.390 120.000 180.000
-0.21735
7 H5 ha E 6 5 4 1.077 120.000 -180.000
0.15052
8 H6 ha E 5 4 3 1.077 120.000 0.000
0.15098
9 C2 ca M 4 3 2 1.394 120.000 -90.000
-0.21801
10 H2 ha E 9 4 3 1.078 120.000 -0.000
0.15098
11 C3 ca M 9 4 3 1.380 120.000 -180.000
-0.21735
12 H3 ha E 11 9 4 1.078 120.000 180.000
0.15052
13 C4 ca M 11 9 4 1.394 120.000 0.000
0.13386
LOOP
C4 C5
IMPROPER
-M C6 C1 C2
C1 C5 C6 H6
C4 C6 C5 H5
C3 C1 C2 H2
C4 C2 C3 H3
+M C3 C4 C5
DONE
STOP
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Received on Sun Apr 30 2006 - 06:07:11 PDT
