[gmx-users] Re: Fatal error: Atomtype F not found

[Justin Lemkul]

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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