[gmx-users] [ atomtypes ] are not case sensitive?

Berk Hess gmx3 at hotmail.com
Mon Aug 18 17:42:07 CEST 2008


In this case at least the non-bonded parameters seem to be the identical.
Are there some different parameters for atom types which only differ in case?
That is bad practice IMHO.
But if so, we should consider changing this or adding an option.


Date: Thu, 14 Aug 2008 14:41:06 +0100
From: alanwilter at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] [ atomtypes ] are not case sensitive?

Playing with amb2gmx.pl, I have in my topol.top file something like:
[snip] C        C           0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860

... c        c           0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860[snip]
Then, running grompp, I got several warnings, e.g.:
WARNING 1 [file "multi_GMX.top", line 38]:
  Overriding atomtype c...

Is there any special reason why atomtypes are not case sensitive? Fortunately it seems that all lower case atomtypes from gaff.dat (GAFF) mirrors the upper case of, say, parm99.dat (AMBER 99). But this is not good in MHO.

Many thanks in advance.
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.

80 Tennis Court Road, Cambridge CB2 1GA, UK.

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