Hi,<br><br>one limitation is that currently both the residue number and the charge group number have to be consecutive in the topology file. Thus if you have a charge group that spans two residues, you need to reorder the atoms, so that the atoms which are part of the spanning group are at the end/beginning of the residue. And if you have a branched molecule - so that one residue can have three spanning charge groups - it does not work. We ended up having to set the residue number to 1 for the whole molecule.<br>
<br>Is this limitation, that residue and charge group have to be consecutive in the topology, necessary?<br><br>Roland<br><br><div class="gmail_quote">On Tue, Mar 3, 2009 at 10:14 AM, Anton Feenstra <span dir="ltr"><<a href="mailto:feenstra@few.vu.nl">feenstra@few.vu.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
The past years we received a lot of requests for Gromacs to preserve the residue numbering of the original pdb file.<br>
Currently Gromacs simply renumbers all residues consecutively starting from one.<br>
I have now implemented free residue numbering (but not committed yet), including pdb insertion codes.<br>
This allows for more freedom, but therefore also some choices nedd to be made.<br>
<br>
A limitation of Gromacs, which I think we would like to preserve, is that residue numbers are stored<br>
per molecule type and therefore one can not have a different numbering in different molecules<br>
of the same type.<br>
</blockquote>
<br></div>
Agreed. This should cover most cases anyway.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
My current implementation preserves the residue numbers for multiple-residue molecules,<br>
but for single residue molecules (for instance water and ions) the residues will continue<br>
numbering from the last residue in the last molecule before.<br>
For a protein in water this gives the most desirable behavior. Although even here there are small<br>
issues. For instance the choice of pdb2gmx writing a gro file with the original pdb res numbers<br>
(e.g. for 2lzm the last prot. resnr is 164, but the first water is 166), which is then not what Gromacs<br>
will produce later, because the tpr made from the top file will number the waters starting at 165.<br>
Should the pdb2gmx output keep the pdb resnrs for the water or use the Gromacs convention?<br>
</blockquote>
<br></div>
I'd say output of pdb2gmx could retain pdb numbering as close as possible, even though subsequent processing might lead to more extensive residue renumbering.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Another effect is that for for instance polymers there will be many residues with resnr 1 in the system.<br>
This is very convenient if you want to select all end groups, but less convenient if you want to select<br>
a particular residue, although this can be done by selecting chains or molecules.<br>
<br>
Finally several analysis tools write values as a function of residue number.<br>
For a single protein it might be very convenient to have the original residue numbers in the output.<br>
But if you have 4 chains, all with resnrs 1 to 200, things get messy.<br>
<br>
Do you have comments or suggestions?<br>
</blockquote>
<br></div>
Perhaps some options could control pdb2gmx behaviour here? Like in your 4-chain example you might want the options to preserve, or number continuously, or add an offset, so chains start at 1, 1001, 2001, 3001?<br>
<br>
Also, adding a 'renumber residues' option to an existing tool (editconf?) might be convenient, to create numbering schemes for different (display) purposes. I vaguely remember seeing such option somewhere, but could not locate it just now.<br>
<br>
-- <br>
Groetjes,<br>
<br>
Anton<br>
_____________ _______________________________________________________<br>
| | |<br>
| _ _ ___,| K. Anton Feenstra |<br>
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |<br>
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| | <a href="mailto:Feenstra@few.vu.nl" target="_blank">Feenstra@few.vu.nl</a> - <a href="http://www.few.vu.nl/%7Efeenstra/" target="_blank">www.few.vu.nl/~feenstra/</a> |<br>
| | "You Could Be a Shadow" (The Breeders) |<br>
|_____________|_______________________________________________________|<div><div><span id="q_11fccf9197ab8060_6" class="h4">- Show quoted text -</span></div><div class="h5"><br>
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