https://wiki.cs.earlham.edu/api.php?action=feedcontributions&user=Hardedo&feedformat=atomEarlham CS Department - User contributions [en]2024-03-28T16:47:27ZUser contributionsMediaWiki 1.32.1https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/&diff=5775Ccg-chemistry-faq/2007-04-10T23:53:20Z<p>Hardedo: </p>
<hr />
<div>Are you having difficulty importing a .pdb or similar file? A simple fix may be available: [[Ccg-chemistry-faq/Protein_Structure_Import_Problems]]<br />
<br />
Is your large molecule crashing due to a lack of memory? Again, a possible fix: [[Ccg-chemistry-faq/Out-of-Memory_Error]]</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/&diff=3059Ccg-chemistry-faq/2007-04-10T23:52:56Z<p>Hardedo: </p>
<hr />
<div>Are you having difficulty importing a .pdb or similar file? A simple fix may be available: [[Protein_Structure_Import_Problems]]<br />
<br />
Is your large molecule crashing due to a lack of memory? Again, a possible fix: [[Out-of-Memory_Error]]</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=5774Ccg-chemistry-faq/Out-of-Memory Error2007-04-10T23:50:41Z<p>Hardedo: </p>
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<div>If after loading a large molecule into WebMO your job quits unexpectedly, you may receive this error message at the bottom of your raw output file:<br />
<br />
''Out-of-memory error in routine ShPair-CalcS2-2 (IEnd=7653401 MxCore=3112170)''<br />
<br />
''Use %mem=11MW to provide the minimum amount of memory required to complete this step.''<br />
<br />
''Error termination via Lnk1e in /cluster/bobsced/g03/l302.exe at (time).''<br />
<br />
<br />
'''To resolve:''' After importing or drawing your molecule, and setting all other options within WebMO to your liking, select the "Preview" tab and press the "generate" button if needed. Then, directly under %NProcShared, insert the following line:<br />
<br />
%mem=20MW <br />
<br />
<br />
This resolves the problem with all molecules tested. If your molecule still returns an error, consider increasing to 25MW.</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3058Ccg-chemistry-faq/Out-of-Memory Error2007-04-10T23:50:20Z<p>Hardedo: </p>
<hr />
<div>If after loading a large molecule into WebMO your job quits unexpectedly, you may receive this error message at the bottom of your raw output file:<br />
<br />
''Out-of-memory error in routine ShPair-CalcS2-2 (IEnd=7653401 MxCore=3112170)''<br />
<br />
''Use %mem=11MW to provide the minimum amount of memory required to<br />
complete this step.''<br />
<br />
''Error termination via Lnk1e in /cluster/bobsced/g03/l302.exe at Tue<br />
Apr 10 09:34:19 2007.''<br />
<br />
<br />
'''To resolve:''' After importing or drawing your molecule, and setting all other options within WebMO to your liking, select the "Preview" tab and press the "generate" button if needed. Then, directly under %NProcShared, insert the following line:<br />
<br />
%mem=20MW <br />
<br />
<br />
This resolves the problem with all molecules tested. If your molecule still returns an error, consider increasing to 25MW.</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3057Ccg-chemistry-faq/Out-of-Memory Error2007-04-10T23:49:55Z<p>Hardedo: </p>
<hr />
<div>If after loading a large molecule into WebMO your job quits unexpectedly, you may receive this error message at the bottom of your raw output file:<br />
<br />
''Out-of-memory error in routine ShPair-CalcS2-2 (IEnd= 7653401<br />
MxCore= 3112170)<br />
<br />
Use %mem=11MW to provide the minimum amount of memory required to<br />
complete this step.<br />
<br />
Error termination via Lnk1e in /cluster/bobsced/g03/l302.exe at Tue<br />
Apr 10 09:34:19 2007.''<br />
<br />
<br />
'''To resolve:''' After importing or drawing your molecule, and setting all other options within WebMO to your liking, select the "Preview" tab and press the "generate" button if needed. Then, directly under %NProcShared, insert the following line:<br />
<br />
%mem=20MW <br />
<br />
<br />
This resolves the problem with all molecules tested. If your molecule still returns an error, consider increasing to 25MW.</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3056Ccg-chemistry-faq/Out-of-Memory Error2007-04-10T23:49:40Z<p>Hardedo: </p>
<hr />
<div>If after loading a large molecule into WebMO your job quits unexpectedly, you may receive this error message at the bottom of your raw output file:<br />
<br />
Out-of-memory error in routine ShPair-CalcS2-2 (IEnd= 7653401<br />
MxCore= 3112170)<br />
<br />
Use %mem=11MW to provide the minimum amount of memory required to<br />
complete this step.<br />
<br />
Error termination via Lnk1e in /cluster/bobsced/g03/l302.exe at Tue<br />
Apr 10 09:34:19 2007.<br />
<br />
<br />
'''To resolve:''' After importing or drawing your molecule, and setting all other options within WebMO to your liking, select the "Preview" tab and press the "generate" button if needed. Then, directly under %NProcShared, insert the following line:<br />
<br />
%mem=20MW <br />
<br />
<br />
This resolves the problem with all molecules tested. If your molecule still returns an error, consider increasing to 25MW.</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Protein_Structure_Import_Problems&diff=5773Ccg-chemistry-faq/Protein Structure Import Problems2007-04-10T23:43:01Z<p>Hardedo: </p>
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<div>WebMO may not properly import your molecule from a .pdb file, depending on how the .pdb was created. For example, for NMR structure determination, sometimes hydrogens are not listed as H but as Q (for reasons we need not get into here). Although visualization programs like PyMOL will work fine, WebMO's import feature doesn't like this very much.<br />
<br />
If your file looks like this, you're OK:<br />
<br />
[[Image:workingpdb.png]]<br />
<br />
<br />
However, if your file looks more like this:<br />
<br />
[[Image:brokenpdb.png]]<br />
<br />
you'll need to make several corrections before proceeding.<br />
<br />
'''1)''' Replace any Qs, as circled above, with H.<br />
<br />
'''2)''' Delete any numbers PRECEEDING an H (any annotation afterwards, like HAX, is fine).<br />
<br />
This should solve basic import problems.</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=File:Workingpdb.png&diff=5772File:Workingpdb.png2007-04-10T23:42:27Z<p>Hardedo: Screenshot of pdb file that is compatible with WebMO</p>
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<div>Screenshot of pdb file that is compatible with WebMO</div>Hardedohttps://wiki.cs.earlham.edu/index.php?title=File:Brokenpdb.png&diff=5771File:Brokenpdb.png2007-04-10T23:42:03Z<p>Hardedo: Screenshot of non-WebMO-compatible pdb file</p>
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<div>Screenshot of non-WebMO-compatible pdb file</div>Hardedo