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 <alanwil...@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 <g...@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: alanwil...@gmail.com >> To: gmx-users@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 <g...@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: alanwil...@gmail.com >> >> To: gmx-users@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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