Thread: [Apbs-users] (no subject)
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: Frank D D. <fr...@it...> - 2003-08-20 06:36:00
|
Does anyone have some suggestions to the following questions: 1) I have been doing calculations on a group of small organic molecules (less than 40 atoms). I have been advised to use either a 1.4 A or 0.0 A solvent radius (srad). Does anyone know which to use? 2) When setting the grid lengths, how much should the grid extend beyound the borders of the molecule? 3) Lastly, after calculating the electrostatic contribution to the total free energy of solvation via APBS, I am now trying to determine the short range contributions to this energu. Does anyone know of any APBS output that may assist me in determining any of the parameters (surface tensions, molecular areas) necessary to calculate this term(s)? Thanks for any help "A hard life is NOT one rife with trial and rigor; but one bereft of option and opportunity." Frank Ducheneaux California Institute of Technology Division of Chemistry M/C 127-72 Pasadena, CA 91125 626-395-2689 (office) |
From: Michael G. <mg...@it...> - 2004-07-28 03:56:39
|
Dear Users, I am solving a system with a kappa map that is identically zero. The kappa map is read into APBS from a previous run; however, I have the counter ion concentration specified in my present file to be (A) non-zero and then (B) zero on the other run. Both solutions use the null kappa map. Should I see a difference in the total energy between A and B? Thanks, Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe |
From: Nathan A. B. <ba...@ch...> - 2004-07-28 13:07:46
|
Hi Michael -- I wouldn't expect a difference but I'd have to see the input file to be sure. Are you seeing different energies? Thanks, Nathan Michael Grabe <mg...@it...> (07-27-2004 18:56:36-0700): >Dear Users, > >I am solving a system with a kappa map that is identically zero. >The kappa map is read into APBS from a previous run; however, >I have the counter ion concentration specified in my present file >to be (A) non-zero and then (B) zero on the other run. >Both solutions use the null kappa map. > >Should I see a difference in the total energy between A and B? > >Thanks, >Michael > >-------------------------------------------------------------------------------------------------- > >Michael Grabe, Ph.D. >HHMI/UCSF >Genetics Development & Behavioral Science Building >1550 4th Street, GD 481 >San Francisco, CA 94143-0725 >tel: ++ 415.476.0421 >http://itsa.ucsf.edu/~mgrabe > > > > End of message from Michael Grabe. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc |
From: James S. <jst...@sc...> - 2005-03-09 00:17:00
|
Hi all, I use the pdb2pqr server to generate pqr and in files for apbs. I can successfully use these files on my powerbook, but it is slow (~ 2days to run for a tetramer). When I try to run apbs on our linux cluster, I get the following log file output..... asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. Then I get the APBS info text and then...... This executable compiled on Mar 8 2005 at 10:45:50 Parsing input file ACUW.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from ACUW.pqr. VASSERT: ASSERTION FAILURE! filename vmem.c, line 245, (ram != 0L) 12526 atoms Centered at (4.999e+01, 3.582e+00, 7.823e+01) Net charge -1.60e+01 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Abort (core dumped) Any clues to the reason for this would be greatly recieved. Best wishes James |
From: Nathan B. <ba...@bi...> - 2005-03-09 14:42:00
|
Hello -- > I use the pdb2pqr server to generate pqr and in files for apbs. Can you provide some statistics on the input files (number of grid pts, grid spacing, etc.)? It sounds like you have a very large system. > I can successfully use these files on my powerbook, but it is slow (~ > 2days to run for a tetramer). > When I try to run apbs on our linux cluster, I get the following log > file output..... > > asc_getToken: Error occurred (bailing out). > Vio_scanf: Format problem with input. This warning message is normal (see other postings to this list) and can be ignored. > Then I get the APBS info text and then...... > > This executable compiled on Mar 8 2005 at 10:45:50 > > Parsing input file ACUW.in... > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from ACUW.pqr. > VASSERT: ASSERTION FAILURE! filename vmem.c, line 245, (ram != 0L) > 12526 atoms > Centered at (4.999e+01, 3.582e+00, 7.823e+01) > Net charge -1.60e+01 e > Preparing to run 4 PBE calculations. > ---------------------------------------- > CALCULATION #1: MULTIGRID > Setting up problem... > Vpbe_ctor: Using max ion radius (2 A) for exclusion function > Abort (core dumped) This error means you ran out of memory. How big was the system and how much memory was available to each processor you used on your cluster? Thanks, Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker |
From: Jean-Marc V. <vui...@bl...> - 2005-08-10 15:05:11
|
Hello, I try to install apbs on a Mac-G5 (osx 10.4) the binary alone are not recognized as a binary through the system, so I can't use them through the shell, and the installation package don't install it, does anyone has the same problems ? any idea to reslove it ? best thanks jean-marc |
From: Todd D. <to...@cc...> - 2005-08-11 15:16:17
|
Hi Jean-Marc - I'm assuming you're referencing the APBS 0.3.2 Mac G5 binary. Once you download the package, can you tell me the exact error message you're getting? The package is in *.pkg.tar.gz format, so you'll have to unzip it first. I think there's a builtin graphical program to do this; if not, open up a shell and unzip the downloaded file (tar -xvzf apbs-0.3.2-g5.pkg.tar.gz) to get the .pkg file itself (apbs-0.3.2-g5.pkg) - then the system should recognize it as an installation package, and all you'll need to do is double click to run the installer, and then proceed to access APBS through the Darwin shell. If this doesn't work, or you're still getting an error message, let me know and we'll see what we can do. Todd Jean-Marc Vuissoz wrote: > Hello, > I try to install apbs on a Mac-G5 (osx 10.4) > the binary alone are not recognized as a binary through the system, so > I can't use them through the shell, > and the installation package don't install it, > does anyone has the same problems ? any idea to reslove it ? > > best thanks > > jean-marc > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |
From: Michael G. <mg...@it...> - 2005-08-15 23:03:37
|
Dear Users, If i ask APBS to calculate the electrostatic potential for a system that is larger than my physical memory, will it fail, or just take a long time to carry out the calculation? thanks michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 482 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe |
From: Nathan B. <sob...@ya...> - 2005-08-16 02:02:25
|
If you exceed the amount of physical memory, APBS (via the Holst group MALOC hardware abstraction library) will use virtual memory -- and therefore will be slow. If you exceed the amount of physical+virtual memory, MALOC will be unable to allocate the necessary memory and APBS will fail with an assertion error. Hope this helps, Nathan --- Michael Grabe <mg...@it...> wrote: > Dear Users, > > If i ask APBS to calculate the electrostatic potential for a system > that is larger than my physical memory, will it fail, or just take > a long time to carry out the calculation? > > thanks > michael > ------------------------------------------------------------------------ > -------------------------- > Michael Grabe, Ph.D. > HHMI/UCSF > Genetics Development & Behavioral Science Building > 1550 4th Street, GD 482 > San Francisco, CA 94143-0725 > tel: ++ 415.476.0421 > http://itsa.ucsf.edu/~mgrabe > > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |
From: Likhatskaya <gal...@pi...> - 2005-12-15 07:17:10
|
Hello apbs-users, confirm 434151 -- Best regards, Likhatskaya mailto:gal...@pi... |
From: Blanton T. <bla...@ur...> - 2006-02-07 18:12:10
|
Hi I am trying to use apbs to calculate the electrostatic surface of an rna molecule. I get the following error message: Parsing input file pymol-generated.in... parsePBE: Warning -- parsed deprecated "bcfl 1" statement parsePBE: Please use "bcfl sdh" instead. NOsh: Warning -- parsed deprecated statment "chgm 1". NOsh: Please use "chgm spl2" instead! parsePBE: Warning -- parsed deprecated "srfm 1" statement. parsePBE: Please use "srfm smol" instead. parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. parsePBE: Please use "calcenergy no" instead. parsePBE: Warning -- parsed deprecated "calcforce 0" statement. parsePBE: Please use "calcforce no" instead. PBEparm_check: SDENS not set! NOsh: MG parameters not set correctly! Error while parsing input file. ObjectMapLoadDXFile-Error: Unable to open file! could some one please provide me some insight into how i can correct this problem. thanks, Blanton Tolbert Graduate Student University of Rochester Biophysics and Structural Biology 585-275-5189 bla...@ur... |
From: Michael G. L. <ml...@um...> - 2006-02-07 18:33:59
|
Hi, Please download and install the most recent version of the PyMOL/APBS Plugin from my webpage (http://www-personal.umich.edu/~mlerner/PyMOL/). The version you're using doesn't work with the current version of APBS. Also, I'm not sure if PyMOL can automatically generate parameters for RNA. If it can't, you might want to use pdb2pqr. -michael -- www.umich.edu/~mlerner | _ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mlerner@umich On Tue, 7 Feb 2006, Blanton Tolbert wrote: > Hi > > I am trying to use apbs to calculate the electrostatic surface of an rna > molecule. I get the following error message: > > Parsing input file pymol-generated.in... > parsePBE: Warning -- parsed deprecated "bcfl 1" statement > parsePBE: Please use "bcfl sdh" instead. > NOsh: Warning -- parsed deprecated statment "chgm 1". > NOsh: Please use "chgm spl2" instead! > parsePBE: Warning -- parsed deprecated "srfm 1" statement. > parsePBE: Please use "srfm smol" instead. > parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. > parsePBE: Please use "calcenergy no" instead. > parsePBE: Warning -- parsed deprecated "calcforce 0" statement. > parsePBE: Please use "calcforce no" instead. > PBEparm_check: SDENS not set! > NOsh: MG parameters not set correctly! > Error while parsing input file. > ObjectMapLoadDXFile-Error: Unable to open file! > > could some one please provide me some insight into how i can correct this > problem. > > thanks, > > > > Blanton Tolbert > Graduate Student > University of Rochester > Biophysics and Structural Biology > 585-275-5189 > bla...@ur... > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > |
From: Todd D. <to...@cc...> - 2006-02-07 20:31:15
|
Hi Michael - I think there may be two different issues here - the deprecated warnings ar= e definitely due to an older version of PyMOL and/or the plugin, but even wit= h the new version of each I duplicate the ObjectMapLoadDXFile-Error: Unable to open file! that others are apparently seeing. Any thoughts? Thanks! Todd On 2/7/06, Michael George Lerner <ml...@um...> wrote: > > > Hi, > > Please download and install the most recent version of the PyMOL/APBS > Plugin from my webpage (http://www-personal.umich.edu/~mlerner/PyMOL/). > The version you're using doesn't work with the current version of APBS. > Also, I'm not sure if PyMOL can automatically generate parameters for RNA= . > If it can't, you might want to use pdb2pqr. > > -michael > > -- > www.umich.edu/~mlerner | _ |Michael Lerner > This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan > it's a cheer-ocracy. | - against HTML email X | Biophysics > -Torrence, Bring It On| / \ | mlerner@umich > > On Tue, 7 Feb 2006, Blanton Tolbert wrote: > > > Hi > > > > I am trying to use apbs to calculate the electrostatic surface of an rn= a > > molecule. I get the following error message: > > > > Parsing input file pymol-generated.in... > > parsePBE: Warning -- parsed deprecated "bcfl 1" statement > > parsePBE: Please use "bcfl sdh" instead. > > NOsh: Warning -- parsed deprecated statment "chgm 1". > > NOsh: Please use "chgm spl2" instead! > > parsePBE: Warning -- parsed deprecated "srfm 1" statement. > > parsePBE: Please use "srfm smol" instead. > > parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. > > parsePBE: Please use "calcenergy no" instead. > > parsePBE: Warning -- parsed deprecated "calcforce 0" statement. > > parsePBE: Please use "calcforce no" instead. > > PBEparm_check: SDENS not set! > > NOsh: MG parameters not set correctly! > > Error while parsing input file. > > ObjectMapLoadDXFile-Error: Unable to open file! > > > > could some one please provide me some insight into how i can correct > this > > problem. > > > > thanks, > > > > > > > > Blanton Tolbert > > Graduate Student > > University of Rochester > > Biophysics and Structural Biology > > 585-275-5189 > > bla...@ur... > > > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |
From: Catherine M. <cat...@fu...> - 2006-05-18 07:42:14
|
Hi I'm trying to use APBS in PYMOL. I have installed the APBS program but I don't find the psize.py file??? what can I do? catherine ############################################################################= ### Michaux Catherine Laboratoire de Chimie Biologique Structurale (CBS) Facult=E9s Universitaires Notre-Dame de la Paix 61, rue de Bruxelles 5000 Namur T=E9l : +32 (0)81/72 45 49 Fax : +32 (0)81/72 45 30 e-mail : cat...@fu... ##################################################=20 ############################# =20 |
From: Vyom S. <vysharma@MIT.EDU> - 2006-05-18 07:47:36
|
I guess it should be in /tools/manip/ directory. On May 18, 2006, at 3:41 AM, Catherine Michaux wrote: > Hi > > I'm trying to use APBS in PYMOL. > > I have installed the APBS program but I don't find the psize.py =20 > file??? > > what can I do? > > catherine > > > > =20 > = #######################################################################=20= > ######## > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Michaux Catherine > Laboratoire de Chimie Biologique Structurale (CBS) > Facult=E9s Universitaires Notre-Dame de la Paix > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 61, rue de Bruxelles=A0=A0=A0=A0=A0=A0 > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 5000 Namur > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 T=E9l : +32 (0)81/72 45 49 > =A0=A0=A0=A0=A0=A0=A0=A0Fax : +32 (0)81/72 45 30 > e-mail : cat...@fu... > =20 > = #######################################################################=20= > ########=20= |
From: Catherine M. <cat...@fu...> - 2006-05-18 10:07:55
|
Hi I'm trying to run APBS from pymol but it doesn't work... So First I open a PQR file (created from a PDB file with pdb2pqr program). Then I set the grid then I run APBS. here find the message: coarsedim is [98.943400000000011, 90.169700000000006, 91.007799999999989] finedim is [78.201999999999998, 73.040999999999997, 73.533999999999992] center is [-14.285, 41.855500000000006, 26.514999999999997] finegridpoints is [129, 129, 129] radiobutton told me to use another Use another=20 PQR so i am returning C:\Program Files\APBS\sqsmoenew11.pqr ObjectMapLoadDXFile-Error: Unable to open file! can you help me? thanks catherine ############################################################################= ### Michaux Catherine Laboratoire de Chimie Biologique Structurale (CBS) Facult=E9s Universitaires Notre-Dame de la Paix 61, rue de Bruxelles 5000 Namur T=E9l : +32 (0)81/72 45 49 Fax : +32 (0)81/72 45 30 e-mail : cat...@fu... ##################################################=20 ############################# =20 |
From: David G. <sd...@gm...> - 2006-05-18 12:15:35
|
Hi Catherine, On May 18, 2006, at 5:06 AM, Catherine Michaux wrote: > > ObjectMapLoadDXFile-Error: Unable to open file! > > can you help me? > This sounds similar to this error: http://sourceforge.net/mailarchive/forum.php? thread_id=10407807&forum_id=46597 Since you can't rename the "Program Files" directory you may want to move the APBS folder and PQR file to a directory path that doesn't include spaces and try executing the program (from within pymol) from there. Regards, Dave David W. Gohara, Ph.D. Center for Computational Biology Washington University School of Medicine http://www.sbgrid.org http://www.macresearch.org 314-362-2934 (phone) 617-216-8616 (cell) |
From: Raul A. <ra...@cg...> - 2006-06-14 17:29:43
|
Dear APBS users: I want to run APBS remotely via the PMV module of APBS. But I don't want to run APBS on any web service, but another Machine here at my lab. But if I just type the IP of such machine I got the following error message.. 192.168.1.123/axis/servlet/AxisServlet could not be found. Please make sure that the server is up and running. I have been looking at the APBS and PMV documentation and I have found nothing about how to set up such a remote calculation. Can any one help me on how to set up my remote machine to work a a server for APBS???? Thanks Raul Araya. Center for Genomics and Bioinformatics P. Catholic University of Chile Santiago Chile |
From: Nathan B. <nat...@wu...> - 2006-06-14 17:56:31
|
That definitely sounds like a PMV issue; I'll Cc Michel and see if he =20= has any ideas. Thanks, Nathan On Jun 14, 2006, at 12:32 PM, Raul Araya wrote: > Dear APBS users: > > > > I want to run APBS remotely via the PMV module of APBS. But I don=92t =20= > want to run APBS on any web service, but another Machine here at my =20= > lab. But if I just type the IP of such machine I got the following =20 > error message=85. > > > > 192.168.1.123/axis/servlet/AxisServlet could not be found. Please =20 > make sure that the server is up and running=85 > > > > I have been looking at the APBS and PMV documentation and I have =20 > found nothing about how to set up such a remote calculation. Can =20 > any one help me on how to set up my remote machine to work a a =20 > server for APBS???? > > > > Thanks > > > > Raul Araya. > > Center for Genomics and Bioinformatics > > P. Catholic University of Chile > > Santiago > > Chile > > > > > > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Sargis D. <sa...@sc...> - 2006-06-14 18:44:46
|
APBS Web Service needs to be installed on the server side before running=20 APBS remotely - http://nbcr.net/services. Please consult APBS Web=20 Service documentation on how to install the server. Thanks, Sargis Nathan Baker wrote: > That definitely sounds like a PMV issue; I'll Cc Michel and see if he =20 > has any ideas. >=20 > Thanks, >=20 > Nathan >=20 > On Jun 14, 2006, at 12:32 PM, Raul Araya wrote: >=20 >=20 >>Dear APBS users: >> >> >> >>I want to run APBS remotely via the PMV module of APBS. But I don=92t =20 >>want to run APBS on any web service, but another Machine here at my =20 >>lab. But if I just type the IP of such machine I got the following =20 >>error message=85. >> >> >> >>192.168.1.123/axis/servlet/AxisServlet could not be found. Please =20 >>make sure that the server is up and running=85 >> >> >> >>I have been looking at the APBS and PMV documentation and I have =20 >>found nothing about how to set up such a remote calculation. Can =20 >>any one help me on how to set up my remote machine to work a a =20 >>server for APBS???? >> >> >> >>Thanks >> >> >> >>Raul Araya. >> >>Center for Genomics and Bioinformatics >> >>P. Catholic University of Chile >> >>Santiago >> >>Chile >> >> >> >> >> >>_______________________________________________ >>apbs-users mailing list >>apb...@li... >>https://lists.sourceforge.net/lists/listinfo/apbs-users >=20 >=20 > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ >=20 >=20 >=20 >=20 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users >=20 >=20 |
From: Timothy D. <mol...@ma...> - 2007-06-05 18:21:26
|
hi, I am using noinput.py (in tools/python) to get my APBS results as python lists. I want to use the lists to assign energies and potentials to each atom in my input structure. I thought the list index corresponded to the atom number, except that the length of the list is not the same as the number of atoms in my input structure. how do I extract a particular atom's energy? thanks for any thoughts, tim -- Timothy Driscoll em: mo...@vb... Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you. |
From: Nathan B. <sob...@gm...> - 2007-06-07 12:08:26
|
Hi Tim -- > I am using noinput.py (in tools/python) to get my APBS results as > python lists. I want to use the lists to assign energies and > potentials to each atom in my input structure. I thought the list > index corresponded to the atom number, except that the length of the > list is not the same as the number of atoms in my input structure. > how do I extract a particular atom's energy? How do the lists differ? Can you send a test case that illustrates the problem? Is this related to the REMARK bug you checked into SF.net? The expected behavior is: for i in range(len(energyList)): list = energyList[i] print "\nPer-atom energies from calculation %i" % i for j in range(len(list)): atom = list[j] print "\t%i\t%.4f kJ/mol" % (j, (float(atom) * factor * 0.5)) i.e., the list indices should correspond to the atom indices. If you can provide details on the differences, we'll check this out. Thanks, Nathan > > thanks for any thoughts, > > tim > -- > Timothy Driscoll em: mo...@vb... > Virginia Bioinformatics Institute ph: 540-231-3007 > Bioinformatics I: M-1 im: molvisions > Washington St., Blacksburg, VA 24061 > > 04-16-07. We will not forget you. > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Timothy D. <mol...@ma...> - 2007-06-07 14:19:34
Attachments:
apbs_lists_issue.tgz
|
On Jun 7, 2007, at 8:08 AM, Nathan Baker wrote: > Hi Tim -- > >> I am using noinput.py (in tools/python) to get my APBS results as >> python lists. I want to use the lists to assign energies and >> potentials to each atom in my input structure. I thought the list >> index corresponded to the atom number, except that the length of the >> list is not the same as the number of atoms in my input structure. >> how do I extract a particular atom's energy? > > How do the lists differ? Can you send a test case that illustrates > the problem? Is this related to the REMARK bug you checked into > SF.net? > hi Nathan, (I am running APBS 0.5.0 on an Apple Intelbook, OS 10.4.9.) for this particular example (1F8W; files attached), the output from noinput.py is 8 entries shorter than the total number of atoms in the pqr file. it is not related to the REMARK bug, as far as I can tell. watching the log stream from APBS, I know it is excluding many atoms for being off the grid - but many more than 8, so I don't think this is the reason. > The expected behavior is: > > for i in range(len(energyList)): > list = energyList[i] > print "\nPer-atom energies from calculation %i" % i > for j in range(len(list)): > atom = list[j] > print "\t%i\t%.4f kJ/mol" % (j, (float(atom) * factor * > 0.5)) > > i.e., the list indices should correspond to the atom indices. If > you can provide details on the differences, we'll check this out. > yes, the above code works fine. looping through by atom, though, is where I run into trouble: def merge(self): """ """ print "Merging APBS data into " + getattr(self.structure, 'id') + "..." for m in self.structure.molecules: for g in m.groups: for a in g.atoms: num = int(getattr(a, 'num')) elist = [] for calc in range(len(self.energies)): e = self.energies[calc][num-1] elist.append(e) setattr(a, 'energies', elist) plist = [] for calc in range(len(self.potentials)): p = self.potentials[calc][num-1] plist.append(p) setattr(a, 'potentials', plist) print "Done." print "" thanks a lot for looking into this. regards, tim -- Timothy Driscoll em: mo...@vb... Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you. |
From: Nathan B. <sob...@gm...> - 2007-06-10 13:45:03
|
Hi Tim -- Todd just checked in changes that affect the issue you reported to our bug tracker (https://sourceforge.net/tracker/? func=detail&atid=771704&aid=1731399&group_id=148472). Can you get the updated version of APBS from SVN (http://sourceforge.net/svn/? group_id=148472) and see if it fixes this issue? Thanks, Nathan On Jun 7, 2007, at 9:18 AM, Timothy Driscoll wrote: > On Jun 7, 2007, at 8:08 AM, Nathan Baker wrote: > >> Hi Tim -- >> >>> I am using noinput.py (in tools/python) to get my APBS results as >>> python lists. I want to use the lists to assign energies and >>> potentials to each atom in my input structure. I thought the list >>> index corresponded to the atom number, except that the length of the >>> list is not the same as the number of atoms in my input structure. >>> how do I extract a particular atom's energy? >> >> How do the lists differ? Can you send a test case that >> illustrates the problem? Is this related to the REMARK bug you >> checked into SF.net? >> > hi Nathan, > > (I am running APBS 0.5.0 on an Apple Intelbook, OS 10.4.9.) > > for this particular example (1F8W; files attached), the output from > noinput.py is 8 entries shorter than the total number of atoms in > the pqr file. it is not related to the REMARK bug, as far as I can > tell. > > watching the log stream from APBS, I know it is excluding many > atoms for being off the grid - but many more than 8, so I don't > think this is the reason. > > >> The expected behavior is: >> >> for i in range(len(energyList)): >> list = energyList[i] >> print "\nPer-atom energies from calculation %i" % i >> for j in range(len(list)): >> atom = list[j] >> print "\t%i\t%.4f kJ/mol" % (j, (float(atom) * factor >> * 0.5)) >> >> i.e., the list indices should correspond to the atom indices. If >> you can provide details on the differences, we'll check this out. >> > > yes, the above code works fine. looping through by atom, though, > is where I run into trouble: > > def merge(self): > """ > """ > > print "Merging APBS data into " + getattr(self.structure, > 'id') + "..." > for m in self.structure.molecules: > for g in m.groups: > for a in g.atoms: > num = int(getattr(a, 'num')) > elist = [] > for calc in range(len(self.energies)): > e = self.energies[calc][num-1] > elist.append(e) > setattr(a, 'energies', elist) > plist = [] > for calc in range(len(self.potentials)): > p = self.potentials[calc][num-1] > plist.append(p) > setattr(a, 'potentials', plist) > print "Done." > print "" > > > > thanks a lot for looking into this. > > > regards, > > tim > -- > Timothy Driscoll em: mo...@vb... > Virginia Bioinformatics Institute ph: 540-231-3007 > Bioinformatics I: M-1 im: molvisions > Washington St., Blacksburg, VA 24061 > > 04-16-07. We will not forget you. > > <apbs_lists_issue.tgz> > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: silvia s. <sil...@gm...> - 2007-12-18 09:08:05
|
please stop sending me these e-mails, I've already solved my problem with APBS. Thanks |