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

Fri Jan 7 10:37:03 CET 2011

Yes. I changed this, since it is required for Amber support with proper atom type names.

But I seem to have forgotten to add it to the 4.5 release notes.

Berk

From: awilter at ebi.ac.uk
Date: Thu, 6 Jan 2011 10:23:25 +0000
To: gmx-users at gromacs.org
CC: 
Subject: [gmx-users] Re: [ atomtypes ] are not case sensitive?

Dear GMX list,
It's more the 2 years ago and now with my gmx.top file containing:
[ atomtypes ];name   bond_type     mass     charge   ptype   sigma         epsilon       Amb

 CA       CA          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860 ca        ca           0.0000  0.0000  A   3.39967e-01  3.59824e-01
And using GMX 4.5 and I don't see this complain anymore:

WARNING 1 [file system_GMX.top, line 43]:  Overriding atomtype CA
Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above?

Many thanks,
Alan 

On 21 August 2008 09:07, Alan <alanwilter at gmail.com> wrote:

Well, I didn't developed Amber FF neither GAFF and although only Amber FF is ported to GMX, one of the greatest appealing of Amber is its antechamber and GAFF for generating topology for non usual compounds.

Looking at the way GAFF was developed (remember G is for generalised) is seemed a natural step to me to use the same name for atom types but using a different cases.
So have said that, I did a look at my converted topology file by amb2gmx/acpypi and found that, although for vdw parameters they seem the same, this doesn't hold for bonds for example. I have this in my GMX top file:

[ bonds ]...96     97   1    1.0800e-01    3.0711e+05 ;    CZ2 - HZ2 (AT CA - HA) Protein
...3154   3194   1    1.0870e-01    2.8811e+05 ;    C76 - H76 (AT ca - ha) Ligand

Anyway, after all this discussion, I realized (correct if I am wrong please) that as long as the vdw parameters are the same, anything else is NOT affected because even for the example of bonds above atom types change nothing since parameters are explicit.

Then, I decided to compare gaff.dat and parm99.dat (topology parameters files for Amber package) for vdw. I did found 2 atom types with same name (diff case though) and diff parameters:

parm99.dat   HP          1.1000  0.0157             Veenstra et al JCC,8,(1992),963   Na          1.8680  0.00277            Na+ Aqvist JPC 1990,94,8021. (adapted)

gaff.dat   hp          0.6000  0.0157             same to hs (be careful !)    na          1.8240  0.1700             OPLS
Observe by the comments (4th column) that although they have the same name (but diff by case) they are completely unrelated, hence the diff values for r0 and epsilon.

So, in the end, at least for example gaff.dat x parm99.dat (note that Amber has several others parm*.dat and glycam*.dat), I do have a conflicting case issue that would affect my topology in GMX format if using amb2gmx/acpypi tool for conversion.

Pondering a bit more, I came to the conclusion that at least for acpypi (which I am developing), I can make it aware of this conflicting atom type naming issue and rename it when converting from Amber to GMX.

About changing something in GMX? Frankly I don't know, but I hope that this thread can be of some use for someone else who stumbles in this problem.
Cheers and many thanks for attention dear Berk.

Alan

From: Berk Hess <gmx3 at hotmail.com>

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

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.