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<div class="moz-cite-prefix">On 02/12/2013 09:05 PM, Mark Abraham
wrote:<br>
</div>
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cite="mid:CAMNuMAQOFra_g0q5OF4z3aeb-jFvhxEAv=ftfTc+uhd4FY8kTA@mail.gmail.com"
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<div class="gmail_quote">On Tue, Feb 12, 2013 at 1:48 PM, Anton
Feenstra <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:k.a.feenstra@vu.nl" target="_blank">k.a.feenstra@vu.nl</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div class="im">On 12/02/13 12:03, Alexey Shvetsov wrote:<br>
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В письме от 12 февраля 2013 11:26:30 пользователь Anton
Feenstra написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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On 11/02/13 17:44, Alexey Shvetsov wrote:<br>
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Hi all!<br>
<br>
Is there a reson why resnames and rtp block names
arent case sensetive?<br>
Actualy I plan to add glycam06.ff port to gromacs. It
has about ~1300 rtp<br>
blocks that are case sensetive.<br>
</blockquote>
<br>
It's error prone, that is the (main) reason they are
case insensitive in<br>
Gromacs. Moreover, in the PDB, anything is (or at least
used to be)<br>
stored in upper case anyway, so there didn't seem to be
any sense in<br>
having lower case (or case sensitive) residue names.<br>
</blockquote>
<br>
Thats true for amino and nucleic acids, but in case for
sugars building block<br>
and glycam resname convention it doesnt work. Also pdb
file format doesnt<br>
states that resname should be case insensetive.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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<br>
Perhaps adding a keyword/switch option in the particular
(rtp/res)<br>
file could enable case sensitive matching on a per file
basis?<br>
</blockquote>
<br>
May be better to enable case sensetive resnames by
default? As it was done<br>
before for atomnames?<br>
</blockquote>
<br>
</div>
Sounds like a good suggestion to me (I didn't<br>
know that atomnames were already case sensitive).</blockquote>
<div><br>
</div>
<div>I can't think of a good reason why not. But I can't think
of someone with the time to do it, either :-)</div>
<div><br>
</div>
<div>Mark </div>
</div>
<br>
</blockquote>
The original reason was that the rtp entry names exactly matched
residue names,<br>
the case of which is not unique. So simply making it case sensitive
will be problematic.<br>
One option could be to first search case sensitive and if no rtp
entry is found for a residue (name)<br>
search case insensitive.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
<br>
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