[gmx-developers] atom types case sensitive

Diana Lousa dlousa at itqb.unl.pt
Wed May 12 11:13:58 CEST 2010


A while ago I noticed that there is an inconsistency in the case type
used for atom type CH2R (which is the atom type of CB, CG and CD in
proline). In the ffG53a5.rtp and ffG53a6.rtp files the atom type is
defined as "CH2R" whereas in the correspondent ffG53*nb.itp files it
is defined as   CH2r. This may an issue to take into acount.

Diana Lousa

On Tue, May 11, 2010 at 8:43 PM,  <hess at sbc.su.se> wrote:
>> On 5/11/10 6:23 PM, Berk Hess wrote:
>>> Hi,
>>> I have made the atom type names case sensitive, because a proper port
>>> of the Amber force fields requires this.
>>> I had to modify the ions.itp file of oplsaa, because there was a case
>>> mismatch.
>>> If someone knows if case sensitivity for atom types (not atom names)
>>> could
>>> cause any issues, please tell me.
>>> Thanks,
>>> Berk
>> This is a strange Amber quirk I guess. Do they use this to distinguis
>> C-alpha and Calcium?
> No. There is a nitrogen type called NA and a sodium type called Na.
> I don't mind having atom types case sensitive. Stricter checking
> on topologies never hurts.
> But we don't want to break any topology processing that is currently
> working.
> Berk
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Diana Lousa
PhD student
Protein Modeling Laboratory
Oeiras, Portugal

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