[gmx-users] Case sensitivity in atomtypes

[Alan]

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