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Dirk<br>
<br>
Lets talk off-line. Can you send me the input that you send to eLBOW?
<br>
<br>
You do need to have GAMESS installed and then you need to do a small
bit of scripting by changing the GAMESS.csh file. I can help with that.<br>
<br>
Nigel<br>
<br>
On 7/3/09 5:27 PM, Dirk wrote:
<blockquote cite="mid:4A4EA1E8.6030507@uni-tuebingen.de" type="cite">
<pre wrap="">Hi,
thanks for the suggestions I tried to run it overnight, but without any
result. I also tried to use GAMESS, but even so the GAMESS run is
started I still get the message "GAMESS doesn't seem to be installed"
and "mv: Aufruf von stat für „elbow.drgfin_pdb.012.gamess.gam“ nicht
möglich: No such file or directory" even so the file exists. Since I'm
not experienced in python I wasn't able to find the reason for that by
inspecting the GAMESSMixins.py script.
I would like to try the forcefield approach, but don't know if there is
any freeware available for that purpose - I would be glad about
suggestions .
For the moment I "solved" the problem by manually editing the cif file
using values from the refmac monomer and link libraries for the
restraints. I still would be really interested in getting elbow to work
to get better restraints for this ligand and to avoid the time consuming
manual creation of cif files in the future.
Thank you again for the replies
Dirk
Schubert, Carsten [PRDUS] schrieb:
</pre>
<blockquote type="cite">
<pre wrap="">What I do in these cases is a MM minimization of the ligand using a high
quality forcefield and using that output as input into elbow and not
perform an optimization, but have it generate the restraints directly
from the input. The differences between the forcefield and the AM1
calculation in elbow are negligible for protein crystallography
purposes. I would not waste time on o.n. runs.
HTH
Carsten
</pre>
<blockquote type="cite">
<pre wrap="">-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> [<a class="moz-txt-link-freetext" href="mailto:phenixbb">mailto:phenixbb</a>-
<a class="moz-txt-link-abbreviated" href="mailto:bounces@phenix-online.org">bounces@phenix-online.org</a>] On Behalf Of Nigel W Moriarty
Sent: Wednesday, July 01, 2009 7:26 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Duration of a phenix.elbow run
Dirk
That is quite a large molecule but it shouldn't take a few hours. I'm
not sure what is happening but I'd guess that a convergence is failing
and the upper limit on the number of steps is too great. If I was
</pre>
</blockquote>
<pre wrap="">you,
</pre>
<blockquote type="cite">
<pre wrap="">I'd run it overnight and if that fails run it in another quantum
package
to get the geometry you desire. A different run MAY generate a
different starting geometry for the --opt option and that may work
better. Each step of the optimisation should take less than 2
</pre>
</blockquote>
<pre wrap="">minutes.
</pre>
<blockquote type="cite">
<pre wrap="">Nigel
On 7/1/09 2:43 PM, Dirk wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I'm trying to create restraints for a carbohydrate ligand using
phenix.elbow. If I run it without the --opt command everything works
fine, but I'm not completely happy with the geometry of my ligand
</pre>
</blockquote>
<pre wrap="">after
</pre>
<blockquote type="cite">
<pre wrap="">refinement. I tried to get an optimized cif by using --opt command,
</pre>
</blockquote>
<pre wrap="">but
</pre>
<blockquote type="cite">
<pre wrap="">the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format)
81 atoms
83 bonds
151 angles
238 dihedrals
--------------------
Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization
</pre>
</blockquote>
<pre wrap="">needs
</pre>
<blockquote type="cite">
<pre wrap="">such a long time and if I let it run overnight (or perhaps longer) I
will get an output or is something going wrong?
The input is a pdb (I tested several) and I tried both the stable
</pre>
</blockquote>
<pre wrap="">phenix
</pre>
<blockquote type="cite">
<pre wrap="">release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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</blockquote>
<pre wrap="">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov
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<pre wrap="">
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<pre wrap=""><!---->
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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