Talk:APBS - Revision history

Pyadmin: 23 revisions

2014-03-28T00:43:59Z

23 revisions

2010-11-05T00:43:18Z

2010-11-04T23:13:24Z

2010-11-04T22:48:17Z

2010-11-04T22:47:07Z

2010-10-29T19:40:44Z

2010-10-29T19:29:43Z

2010-10-29T19:27:58Z

2010-10-29T16:58:27Z

2010-10-29T16:57:19Z

Running with APBS 1.3

← Older revision		Revision as of 00:43, 5 November 2010
Line 99:		Line 99:
	Could not generate PQR file!		Could not generate PQR file!
	--[[User:Rendereason\|Rendereason]] 22:48, 4 November 2010 (UTC)		--[[User:Rendereason\|Rendereason]] 22:48, 4 November 2010 (UTC)
		+
		+	OK, I think I know what's causing at least some of the problems. I find email a lot easier than wiki pages for sorting all of this out. Can you send a list of the current errors you're getting along with your PyMOL version, APBS version, PDB2PQR version and operating system to me at my gmail account (mglerner)? Thanks! --[[User:Mglerner\|michael]] 00:43, 5 November 2010 (UTC)

@@ Line 86: / Line 86: @@
 Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)
-Yes. I have. Also, I get this problem:
+Yes. Those errors happen with the pre-release version you posted. It also ignores the binary I have configured it to use in /usr/local/apbs/bin/ for the fink one in /sw64/bin/.
    GENERATING PQR FILE via PDB2PQR
    Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file

@@ Line 85: / Line 85: @@
 Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)
 Yes. I have. Also, I get this problem:
-GENERATING PQR FILE via PDB2PQR
+  GENERATING PQR FILE via PDB2PQR
-Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
+  Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
-Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
+  Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
-TESTING
+  TESTING
-DONE TESTING
+  DONE TESTING
-Appended /sw64
+  Appended /sw64
-Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
+  Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
-In show error 2
+  In show error 2
-Could not generate PDB2PQR file.  _generatePdb2pqrPqrFile failed.
+  Could not generate PDB2PQR file.  _generatePdb2pqrPqrFile failed.
-Could not generate PQR file!
+  Could not generate PQR file!

← Older revision		Revision as of 22:47, 4 November 2010
Line 85:		Line 85:

	Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner\|michael]] 19:40, 29 October 2010 (UTC)		Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner\|michael]] 19:40, 29 October 2010 (UTC)
		+	Yes. I have. Also, I get this problem:
		+	GENERATING PQR FILE via PDB2PQR
		+	Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
		+	Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
		+	TESTING
		+	DONE TESTING
		+	Appended /sw64
		+	Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
		+	In show error 2
		+	Could not generate PDB2PQR file. _generatePdb2pqrPqrFile failed.
		+	Could not generate PQR file!

← Older revision		Revision as of 19:40, 29 October 2010
Line 83:		Line 83:
	Changing the parameters within apbsplugin.py to their desired folders gives the error above.		Changing the parameters within apbsplugin.py to their desired folders gives the error above.
	--[[User:Rendereason\|Rendereason]] 16:57, 29 October 2010 (UTC)		--[[User:Rendereason\|Rendereason]] 16:57, 29 October 2010 (UTC)
		+
		+	Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner\|michael]] 19:40, 29 October 2010 (UTC)

← Older revision	Revision as of 00:43, 28 March 2014
(No difference)

@@ Line 70: / Line 70: @@
 I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)
-I found out:
+The installation guide says:
 "The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
 I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
@@ Line 80: / Line 80: @@
    export APBS_BINARY_DIR
    export APBS_PSIZE_DIR
-None of this works.
+None of this had any effect on the unmodified apbsplugin.py. (When parameters set to ''None'')
 --[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

@@ Line 53: / Line 53: @@
 '''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)
-==Running with APBS 1.3==
+==Running with APBS 1.3 not working==
 Well, I tried making the plugin run with APBS 1.3 and this is what I got:
    Running:
@@ Line 72: / Line 72: @@
 I found out:
 "The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
-So maybe ${APBS_PREFIX} is what needs to be fixed. I'll try that.--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)
+I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.

← Older revision		Revision as of 16:57, 29 October 2010
Line 69:		Line 69:

	I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason\|Rendereason]] 16:49, 29 October 2010 (UTC)		I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason\|Rendereason]] 16:49, 29 October 2010 (UTC)
		+
		+	I found out:
		+	"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution."
		+	So maybe ${APBS_PREFIX} is what needs to be fixed. I'll try that.--[[User:Rendereason\|Rendereason]] 16:57, 29 October 2010 (UTC)