[gmx-users] Case sensitivity in atomtypes

[Baptiste Demoulin]

Thank you for your answers,

I finally added "l" at the end of the names of the atoms, which seemed to
be the easiest solution. For most of the computation, having these
[bondtypes] like entries was not mandatory, but I wanted to import the
topologies in pDynamo, which requires such a "database".

Thank you again !

Baptiste


2013/6/7 Alan <alanwilter at gmail.com>

> I may not got the question properly but when I designed ACPYPE, I had
> similar issues and for that reason I created this option:
>
>
> -g, --disambiguate    disambiguate lower and uppercase atomtypes in GMX top
>                         file
>
> So try your usual acpype command with "-g" option.
>
> BTW, acpype -h can show you many more interesting options.
>
> Alan
>
>
> On 7 June 2013 15:55, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
> > <bat.demoulin at gmail.com>wrote:
> >
> > > Hello GMX users,
> > >
> > > I have some troubles with overriding parameters. I have generated
> > > parameters for lipids using Lipid11 forcefield for AMBER, based on
> GAFF,
> > > and Acpype. This forcefield contains atomtypes cA, cB for instance.
> When
> > I
> > > include the bonded parameters in [bondtypes], [angletypes] sections of
> my
> > > topology, or alternatively in ffbonded.itp, grompp returns warning
> > > concerning overriding of bonds and angles involving CA, CB, HA, ...
> > (AMBER
> > > atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA,
> ...).
> > >
> > > WARNING 1 [file ffbonded.itp, line 222]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.137 435136 0.137 435136     <------- VALUE FOR AMBER FF FOR
> > CB-CB
> > > BOND
> > >   new: cB     cB   1    1.3240e-01    4.9346e+05 <------- VALUE FOR
> > LIPID11
> > > cB-cB
> > >
> > >
> > > WARNING 2 [file ffbonded.itp, line 225]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.1404 392459 0.1404 392459
> > >   new: cA     cB   1    1.5080e-01    2.7472e+05
> > >
> > >
> > > WARNING 3 [file ffbonded.itp, line 227]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.1381 357314 0.1381 357314
> > >   new: nA     cA   1    1.4990e-01    2.4568e+05
> > >
> > >
> > > WARNING 4 [file ffbonded.itp, line 228]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.108 307106 0.108 307106
> > >   new: cA     hA   1    1.0920e-01    2.8225e+05
> > >
> > >
> > > WARNING 5 [file ffbonded.itp, line 229]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.14 392459 0.14 392459
> > >   new: cA     cA   1    1.5350e-01    2.5363e+05
> > >
> > >
> > > WARNING 6 [file ffbonded.itp, line 760]:
> > >   Overriding Angle parameters.
> > >
> > >   old: 120 527.184 120 527.184
> > >   new: cA     cA     cA   1    1.1063e+02    5.2894e+02
> > >
> > >
> > > WARNING 7 [file ffbonded.itp, line 773]:
> > >   Overriding Angle parameters.
> > >
> > >   old: 120 527.184 120 527.184
> > >   new: cB     cA     cA   1    1.1144e+02    5.3162e+02
> > >
> > >
> > > WARNING 8 [file ffbonded.itp, line 783]:
> > >   Overriding Angle parameters.
> > >
> > >   old: 117.3 527.184 117.3 527.184
> > >   new: cB     cB     cA   1    1.2342e+02    5.3831e+02
> > >
> > >
> > > WARNING 9 [file ffbonded.itp, line 788]:
> > >   Overriding Angle parameters.
> > >
> > >   old: 120 418.4 120 418.4
> > >   new: cA     cA     hA   1    1.1005e+02    3.8802e+02
> > >
> > >
> > > WARNING 10 [file ffbonded.itp, line 794]:
> > >   Overriding Angle parameters.
> > >
> > >   old: 120 418.4 120 418.4
> > >   new: hA     cA     cB   1    1.1049e+02    3.9355e+02
> > >
> > > Aren't Atomtypes supposed to be case sensitive ?
> > >
> >
> > Probably not, when pdb2gmx was designed.
> >
> > Using a case-sensitive tool like sed (or perl, or python) to re-name "cA"
> > to "LcA" or something is probably the best solution. But don't break the
> > fixed-column requirements of your coordinate files!
> >
> > Mark
> > --
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>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
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