[gmx-users] Re: [ atomtypes ] are not case sensitive?
Alan Wilter Sousa da Silva
awilter at ebi.ac.uk
Thu Jan 6 11:23:25 CET 2011
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.
>> But allowing this probably does not mean that many people would do this.
>>
>> Another option would be to add an option to grompp.
>>
>> Berk.
>>
>>
>> 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.
>>
>>
>>
>> Berk.
>>
>>
>>
>>
>>
>> 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?
>>
>>
>>
>> Dears,
>>
>> 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.
>>
>> Cheers,Alan
>>
>>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
--
Alan Wilter SOUSA da SILVA, D.Sc.
Bioinformatician, UniProt - PANDA, EBI-EMBL
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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