[gmx-users] grompp warning - serious or not?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 1 15:23:04 CET 2005
On Tue, 2005-03-01 at 13:51 +0000, Samantha Kaye wrote:
> I found out that is was the CH3 - C - O angle of my ACE cap that it was
> complaining about.
> I also found out that this should be a ga_30 type angle but that this
> angle isn't defined in the ffG53a6.rtp file.
> I added the angle type directly to the protein.itp file and now it runs.
> Did I do anything I shouldn't have here? Is there any particular reason
> why the angle in missing from the rtp file?
Because standard gromos does not support ACE I presume. You have done
"the right thing" (tm).
> Regards
> Sam
>
> David van der Spoel wrote:
>
> >On Tue, 2005-03-01 at 10:57 +0000, Samantha Kaye wrote:
> >
> >
> >>Hi,
> >>I have been getting this warning when running grompp in gromacs 3.2.1
> >>and using the ffG53a6 forcefield:
> >>WARNING 2 [file "1S50_protein.itp", line 9698]:
> >> No default G96Angle types, using zeroes
> >>Excluding 3 bonded neighbours for Protein 1
> >>Excluding 3 bonded neighbours for GLT 1
> >>Excluding 1 bonded neighbours for HOH 359
> >>Excluding 2 bonded neighbours for SOL 24471
> >>
> >>Is this a serious problem or should I ignore it?
> >>
> >>
> >Yes. Fix it.
> >
> >
> >>TIA
> >>Sam
> >>_______________________________________________
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> >>
> >>
> >--
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596, 75124 Uppsala, Sweden
> >phone: 46 18 471 4205 fax: 46 18 511 755
> >spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> --
> ***********************************************************************
> Samantha L. Kaye e-mail: samantha at biop.ox.ac.uk
> Lab. of Molecular Biophysics phone: 01865-275275
> Dept. of Biochemistry fax: 01865-275182
> University of Oxford
> South Parks Road http://sansom.biop.ox.ac.uk/samantha
> Oxford
> OX1 3QU
> U.K.
> ***********************************************************************
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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