Thread: [Apbs-users] PQR File Problem!
Biomolecular electrostatics software
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From: <vin...@dr...> - 2006-09-07 18:11:03
Attachments:
boxTest00-00
hpin_unfold-SA.pqr
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Hi --- I'm having trouble running a pqr file that I generated from a pdb file (originally made with the nucleic acid builder). I've checked but can't really seem to find anything overtly wrong with the structure file. I've attached the PQR file as well as the apbs input file. The error message I'm getting is: Parsing input file boxTest00-00... asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from unfold_test.pqr. Valist_readPQR: Error parsing ATOM field! Error while reading molecule from unfold_test.pqr Error reading molecules! thanks, Vince |
From: Todd D. <to...@cc...> - 2006-09-08 15:52:17
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Hi Vince - It's most likely due to fields merging together, for example the x and y fields here: ATOM 887 C2' G 28 1.206 -5.157-126.631 -0.1800 2.0100 Since APBS uses token-based parsing rather than column-based parsing, it will fail on these fields. If you add a space before each "-" sign it should resolve this issue. We'll hopefully have this resolved in either PDB2PQR/APBS (or both) in the near future. Todd On 9/7/06, vin...@dr... <vin...@dr...> wrote: > > Hi --- > > I'm having trouble running a pqr file that I generated from a pdb file > (originally made with the nucleic acid builder). I've checked but can't > really seem to find anything overtly wrong with the structure file. > > I've attached the PQR file as well as the apbs input file. The error > message I'm getting is: > > Parsing input file boxTest00-00... > asc_getToken: Error occurred (bailing out). > Vio_scanf: Format problem with input. > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from unfold_test.pqr. > Valist_readPQR: Error parsing ATOM field! > Error while reading molecule from unfold_test.pqr > Error reading molecules! > > > thanks, > > Vince > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > |
From: Andreas Svrcek-S. <sv...@tb...> - 2006-09-08 16:04:41
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Hi, > I'm having trouble running a pqr file that I generated from a pdb file > (originally made with the nucleic acid builder). I've checked but can't > really seem to find anything overtly wrong with the structure file. > > I've attached the PQR file as well as the apbs input file. The error message > I'm getting is: ...what I saw: 1) "q" and "r" column have too many digits ...I don't know whether this could have caused your trouble 2) I had a look with VMD -> the stucture seems totally corrupt with quite a lot of bad contacts. good luck Andreas |
From: Nathan B. <sob...@gm...> - 2006-09-08 18:41:07
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Hi All -- > 2) I had a look with VMD -> the stucture seems totally corrupt with > quite a lot of bad contacts. According to John Stone (VMD), VMD often draws strange bonds from PQR files because it attempts to interpret bond information from the radii. We've talked in the past about how to circumvent some of these bonding problems by reading the PQR files in as PDBs. I'll Cc John to see if he can provide some more specific tips. Thanks, Nathan > good luck > Andreas > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > 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: John S. <jo...@ks...> - 2006-09-08 18:50:52
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Hi, Nathan is correct that the automatic bond determination code in VMD is sensitive to radii, and the radii used in PQR files are frequently large enough to cause this type of problem. Going further, these large radii can also cause problems for programs like MSMS (solvent surface engine developed at Scripps) because the radii can be large enough that some atoms actually fall completely within the radius of others, which is "illegal" from the point of view of MSMS. So, the upshot of this is that the radii contained in the PQR files may cause trouble for various other packages. In VMD you can work around this either by forcing VMD to load the PQR file as a PDB (which will cause VMD to use its own simple radius determination code), or by running the AutoPSF structure building plugin which will automatically build a PSF file which contains explicit bond information based on CHARMM topology information. Let me know if you need help with this. John Stone vm...@ks... On Fri, Sep 08, 2006 at 01:41:01PM -0500, Nathan Baker wrote: > Hi All -- > > >2) I had a look with VMD -> the stucture seems totally corrupt with > >quite a lot of bad contacts. > > According to John Stone (VMD), VMD often draws strange bonds from PQR > files because it attempts to interpret bond information from the > radii. We've talked in the past about how to circumvent some of > these bonding problems by reading the PQR files in as PDBs. I'll Cc > John to see if he can provide some more specific tips. > > Thanks, > > Nathan > > >good luck > >Andreas > > > >---------------------------------------------------------------------- > >--- > >Using Tomcat but need to do more? Need to support web services, > >security? > >Get stuff done quickly with pre-integrated technology to make your > >job easier > >Download IBM WebSphere Application Server v.1.0.1 based on Apache > >Geronimo > >http://sel.as-us.falkag.net/sel? > >cmd=lnk&kid=120709&bid=263057&dat=121642 > >_______________________________________________ > >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/ > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: jo...@ks... Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 |