AMBER Archive (2006)

Subject: AMBER: How to build 1,4-dimethyl benzene with amber9

From: martin peters (peters_at_ufl.edu)
Date: Fri Apr 28 2006 - 16:27:09 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu