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

shika pqah123 at gmail.com
Thu Oct 4 11:05:25 CEST 2012

Thanks David for your help.But then I already change by using the
script that i found in google.
After I changed the charge which that from the RESP calculation. The
problem start occur when i already changed the atom type according to
the oplsaa force field and the error come out said that not recognized
the F atom.Is that I made mistake when change the atom type?

Thanks again for the website that you gave to me but I had one
question for my type hexafluoroisopropanol which the model already
produced by Fioroni where a lot of researcher used his model as their
simulation part.Can you help me how I can find this model?Like your
website that already produce the organic molecules.Unfortunately my
organic is not there..

Thanks in advance,

On 10/4/12, David van der Spoel [via GROMACS]
<ml-node+s5086n5001591h5 at n6.nabble.com> wrote:
> On 2012-10-04 04:39, Nur Syafiqah Abdul Ghani wrote:
>> Dear Users,
>> Right now i already done for creating the a gro file from antechamber
>> to gromacs format of my molecule which is hexafluoroisopropanol.
>> But when i want to minimize it in vacuum it show atomtype F not found.
>> Im using oplsaa force field and i already change the atom type
>> according to the force field.
> Do not combine force fields. Use antechamber and the gromacs conversion
> script to make a gromacs topology from it (amb2gmx.pl, search on
> google), then use amber force field in combination with this if you want
> to dissolve biomolecules or something like that.
> More organic molecules topologies can be found at
> http://virtualchemistry.org
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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