On 10/3/12 11:41 PM, shika wrote:
Thanks for fast reply.I am very new to this and yes I am confused
my itp file is :
; solvent_HFI.gro.top created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
;
;
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge
mass typeB chargeB
1 opls_164 1 HFI F 1 -0.234745
19.000000
2 opls_161 1 HFI C 2 0.705532
12.000000
3 opls_164 1 HFI F1 3 -0.205102
19.000000
4 opls_164 1 HFI F2 4 -0.237125
19.000000
5 opls_158 1 HFI C1 5 -0.119035
12.000000
6 opls_078 1 HFI O 6 -0.600958
16.000000
7 opls_079 1 HFI H1 7 0.468121
1.000000
8 opls_140 1 HFI H 8 0.141115
1.000000
9 opls_161 1 HFI C2 9 0.786317
12.000000
10 opls_164 1 HFI F4 10 -0.230854
19.000000
11 opls_164 1 HFI F5 11 -0.266972
19.000000
12 opls_164 1 HFI F3 12 -0.206295
19.000000
[ bonds ]
; ai aj funct
5 8 1
6 7 1
1 2 1
2 3 1
2 4 1
2 5 1
5 6 1
5 9 1
9 10 1
9 11 1
9 12 1
[ pairs ]
; ai aj funct
1 8 1
2 7 1
3 8 1
4 8 1
7 8 1
7 9 1
8 10 1
8 11 1
8 12 1
1 6 1
1 9 1
2 10 1
2 11 1
2 12 1
3 6 1
3 9 1
4 6 1
4 9 1
6 10 1
6 11 1
6 12 1
[ angles ]
; ai aj ak funct
2 5 8 1
5 6 7 1
6 5 8 1
8 5 9 1
1 2 3 1
1 2 4 1
1 2 5 1
2 5 6 1
2 5 9 1
3 2 4 1
3 2 5 1
4 2 5 1
5 9 10 1
5 9 11 1
5 9 12 1
6 5 9 1
10 9 11 1
10 9 12 1
11 9 12 1
[ dihedrals ]
;i j k l func
1 2 5 8 3
2 5 6 7 3
3 2 5 8 3
4 2 5 8 3
7 6 5 8 3
7 6 5 9 3
8 5 9 10 3
8 5 9 11 3
8 5 9 12 3
1 2 5 6 3
1 2 5 9 3
2 5 9 10 3
2 5 9 11 3
2 5 9 12 3
3 2 5 6 3
3 2 5 9 3
4 2 5 6 3
4 2 5 9 3
6 5 9 10 3
6 5 9 11 3
6 5 9 12 3
I would be grateful if you could highlight things that need to be edited.
There is no atomtype F referenced in this topology, so the source of the error
is still unclear.
One more thing,is OPLSAA forcefield suitable for my non standard molecule?
Any force field can be used for any molecule, provided the parameterization was
done thoroughly and evaluated properly. The header of your topology suggests
you used an AMBER conversion script, so you may be mixing and matching
parameters here, which is a bad idea.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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