[gmx-users] Case sensitivity in atomtypes

[Mark Abraham]

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