[gmx-users] Re: Fatal error: Atomtype F not found
Justin Lemkul
jalemkul at vt.edu
Thu Oct 4 14:19:18 CEST 2012
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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