https://wiki.cs.earlham.edu/api.php?action=feedcontributions&user=Hardedo&feedformat=atom Earlham CS Department - User contributions [en] 2024-03-28T16:47:27Z User contributions MediaWiki 1.32.1 https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/&diff=5775 Ccg-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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/&diff=3059 Ccg-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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=5774 Ccg-chemistry-faq/Out-of-Memory Error 2007-04-10T23:50:41Z <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 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 &quot;Preview&quot; tab and press the &quot;generate&quot; 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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3058 Ccg-chemistry-faq/Out-of-Memory Error 2007-04-10T23:50:20Z <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 &quot;Preview&quot; tab and press the &quot;generate&quot; 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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3057 Ccg-chemistry-faq/Out-of-Memory Error 2007-04-10T23:49:55Z <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 &quot;Preview&quot; tab and press the &quot;generate&quot; 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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Out-of-Memory_Error&diff=3056 Ccg-chemistry-faq/Out-of-Memory Error 2007-04-10T23:49:40Z <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 &quot;Preview&quot; tab and press the &quot;generate&quot; 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> Hardedo https://wiki.cs.earlham.edu/index.php?title=Ccg-chemistry-faq/Protein_Structure_Import_Problems&diff=5773 Ccg-chemistry-faq/Protein Structure Import Problems 2007-04-10T23:43:01Z <p>Hardedo: </p> <hr /> <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> Hardedo https://wiki.cs.earlham.edu/index.php?title=File:Workingpdb.png&diff=5772 File:Workingpdb.png 2007-04-10T23:42:27Z <p>Hardedo: Screenshot of pdb file that is compatible with WebMO</p> <hr /> <div>Screenshot of pdb file that is compatible with WebMO</div> Hardedo https://wiki.cs.earlham.edu/index.php?title=File:Brokenpdb.png&diff=5771 File:Brokenpdb.png 2007-04-10T23:42:03Z <p>Hardedo: Screenshot of non-WebMO-compatible pdb file</p> <hr /> <div>Screenshot of non-WebMO-compatible pdb file</div> Hardedo