Dear GMX list,<div><br></div><div>It's more the 2 years ago and now with my gmx.top file containing:</div><div><br></div><div><div>[ atomtypes ]</div><div>;name bond_type mass charge ptype sigma epsilon Amb</div>
<div> CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860</div><div> ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01</div><div><br></div><div>And using GMX 4.5 and I don't see this complain anymore:</div>
<div><br></div><div><div>WARNING 1 [file system_GMX.top, line 43]:</div><div> Overriding atomtype CA</div></div><div><br></div><div>Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above?</div>
<div><br></div><div>Many thanks,</div><div><br></div><div>Alan </div><div><br></div><br><div class="gmail_quote">On 21 August 2008 09:07, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div dir="ltr"><div class="gmail_quote"><div>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.</div>
<div><br></div><div>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.</div><div><br></div><div>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:</div>
<div><br></div><div>[ bonds ]</div><div>...</div><div>96 97 1 1.0800e-01 3.0711e+05 ; CZ2 - HZ2 (AT CA - HA) Protein<br></div><div>...</div><div>3154 3194 1 1.0870e-01 2.8811e+05 ; C76 - H76 (AT ca - ha) Ligand<br>
</div><div><br></div><div>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.</div>
<div><br></div><div>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:</div><div><br>
</div><div>parm99.dat</div><div><div> HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963</div><div> Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)</div><div><br></div>
<div>gaff.dat</div><div><div> hp 0.6000 0.0157 same to hs (be careful !) </div><div> na 1.8240 0.1700 OPLS</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div><div>Cheers and many thanks for attention dear Berk.</div>
<div><br></div><div>Alan</div><div><br></div></div></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">From: Berk Hess <<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>><br>
</div>
Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive?<br>Hi,<br>
<br>
I don't know if any thinking went into the (non) case specifity of atom types.<br>
Nearly all string comparisons in Gromacs are not case specific.<br>
For things like atom names this makes sense.<br>
<br>
We could change the atom type comparisons to case specific.<br>
I think that all force field files supplied with Gromacs have consistent cases.<br>
But some users might have made force fields where this would cause problems.<br>
<br>
I think it is bad practice to distinguish atom types just by case,<br>
this makes things quite error prone.<br>
But allowing this probably does not mean that many people would do this.<br>
<br>
Another option would be to add an option to grompp.<br>
<br>
Berk.<br>
<br>
<br>
Date: Tue, 19 Aug 2008 12:03:57 +0100<div class="im"><br>
From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive?<div><div></div><div class="h5"><br>
<br>
Dear Berk,<br>
Thanks for your attention.<br>
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).<br>
<br>
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.<br>
<br>
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!<br>
<br>
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.<br>
<br>
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?<br>
<br>
From: Berk Hess <<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>><br>
In this case at least the non-bonded parameters seem to be the identical.<br>
<br>
Are there some different parameters for atom types which only differ in case?<br>
<br>
<br>
Hence, I don't have a clear example to answer your question, but I am investigating. Cheers,Alan<br>
<br>
That is bad practice IMHO.<br>
<br>
But if so, we should consider changing this or adding an option.<br>
<br>
<br>
<br>
Berk.<br>
<br>
<br>
<br>
<br>
<br>
Date: Thu, 14 Aug 2008 14:41:06 +0100<br>
<br>
From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br>
<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>
Subject: [gmx-users] [ atomtypes ] are not case sensitive?<br>
<br>
<br>
<br>
Dears,<br>
<br>
Playing with <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a>, I have in my topol.top file something like:<br>
<br>
[snip] C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860<br>
<br>
<br>
<br>
... c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860[snip]<br>
<br>
Then, running grompp, I got several warnings, e.g.:<br>
<br>
WARNING 1 [file "multi_GMX.top", line 38]:<br>
<br>
Overriding atomtype c...<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
<br>
Many thanks in advance.<br>
<br>
Cheers,Alan<br>
<br></div></div></blockquote></div><div><div></div><div class="h5"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter SOUSA da SILVA, D.Sc.<div>Bioinformatician, UniProt - PANDA, EBI-EMBL<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
</div>