Abhishek Banerjee wrote:
Hi,
After long try and error and with some reference I made a
topology of DMF with six site interaction using OPLS/AA and topolgen.
Can some tell me is it the correct format of a topology file or do i
need to consider any other fact.
Well, having written the script, I can tell you that the format is correct. As
for the validity of its contents, that is up to you based on whatever model
you're trying to use.
I would say, however, that there is one very obvious error: your molecule has a
net charge of 0.020.
-Justin
;
; OPLS-AA topology, built by TopolGen version 1.0 (3/21/2009)
; Script written by: Justin Lemkul ([email protected])
; This is your molecule's topology
; Check it carefully for any errors. It is not necessarily perfect!
;
; Topology written on Sun Sep 6 15:41:15 IST 2009
;
; Include force field
#include "ffoplsaa.itp"
[ atomtypes ]
C3 15.03500 0.285 A 3.80000e-01 7.11280e-01
N 14.00670 -0.570 A 3.25000e-01 7.11280e-01
C 12.01100 0.500 A 3.80000e-01 4.81160e-01
H 1.00800 0.020 A 2.50000e-01 1.25520e-01
O 15.99940 -0.500 A 2.96000e-01 8.78640e-01
[ moleculetype ]
; Name nrexcl
DMF 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 C3 1 DMF CM1 1 0.285
12.01100
2 N 1 DMF NM 1 -0.570
14.00670
3 C3 1 DMF CM2 1 0.285
12.01100
4 C 1 DMF CF 1 0.500
12.01100
5 H 1 DMF HF 1 0.020
1.00800
6 O 1 DMF OF 1 -0.500
15.99940
[ bonds ]
; ai aj funct
1 2 1 0.14490 282001.6
2 3 1 0.14490 282001.6
2 4 1 0.13350 410032.0
4 5 1 0.10900 284512.0
4 6 1 0.12290 476976.0
[ pairs ]
; ai aj funct
1 5 1
1 6 1
3 5 1
3 6 1
[ angles ]
; ai aj ak funct
1 2 3 1 116.200 711.280
1 2 4 1 121.900 418.400
3 2 4 1 121.900 418.400
2 4 5 1 109.500 292.880
2 4 6 1 122.900 669.440
5 4 6 1 123.000 292.880
[ dihedrals ]
; ai aj ak al funct
1 2 4 5 3 -0.29079 -0.87237 0.00000
1.16315 0.00000 0.00000
1 2 4 6 3 25.47638 0.00000 -25.47638
0.00000 0.00000 0.00000
3 2 4 5 3 -0.29079 -0.87237 0.00000
1.16315 0.00000 0.00000
3 2 4 6 3 25.47638 0.00000 -25.47638
0.00000 0.00000 0.00000
[ dihedrals ]
; aj ak ai al funct
1 3 2 4 1 improper_Z_N_X_Y
2 6 4 5 1 improper_O_C_X_Y
[ system ]
; Name
DMF, generated by TopolGen
[ molecules ]
; Compound #mols
DMF 1
Thanks
abhishek
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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