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

Berk Hess gmx3 at hotmail.com
Tue Aug 19 13:47:56 CEST 2008


I don't know if any thinking went into the (non) case specifity of atom types.
Nearly all string comparisons in Gromacs are not case specific.
For things like atom names this makes sense.

We could change the atom type comparisons to case specific.
I think that all force field files supplied with Gromacs have consistent cases.
But some users might have made force fields where this would cause problems.

I think it is bad practice to distinguish atom types just by case,
this makes things quite error prone.
But allowing this probably does not mean that many people would do this.

Another option would be to add an option to grompp.


Date: Tue, 19 Aug 2008 12:03:57 +0100
From: alanwilter at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive?

Dear Berk,
Thanks for your attention.
I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi).

So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. 

If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said before, I am not 100% sure about it. However, for Amber MD, case matters!

Anyway, I am just worried about integrating Amber FF in GMX. If using ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I add a ligand.itp build with help of antechamber with GAFF to my system, the AT types will never conflict with ffamber*.itp.

So, to summarise, I am really concerned that GMX is not case sensitive in the matter of AT. Is there any special reason for doing so?

From: Berk Hess <gmx3 at hotmail.com> 
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?

Hence, I don't have a clear example to answer your question, but I am investigating.  Cheers,Alan

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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