[gmx-users] RE: [ atomtypes ] are not case sensitive?
alanwilter at gmail.com
Tue Aug 19 13:03:57 CEST 2008
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
Hence, I don't have a clear example to answer your question, but I am
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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