Thread: [Apbs-users] pqr file format
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From: Jianghai Z. <jia...@um...> - 2007-10-18 21:39:00
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Hi all, I generated a pqr file using pdb2pqr webserver. when I ran apbs 0.5.1, I got the following error. Parsing input file I-like.pqr.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from I-like.pqr. Valist_readPQR: Error parsing ATOM field! Error while reading molecule from I-like.pqr Error reading molecules! My pqr file looks like this. ATOM 1 N ASP 109 -61.710-104.919 -76.847 -0.30 1.850 ATOM 2 CA ASP 109 -63.015-105.565 -76.644 0.21 2.275 ATOM 3 C ASP 109 -63.850-104.951 -75.482 0.51 2.000 ATOM 4 O ASP 109 -64.777-105.570 -74.978 -0.51 1.700 ATOM 5 CB ASP 109 -62.817-107.080 -76.428 -0.28 2.175 ATOM 6 CG ASP 109 -64.137-107.829 -76.243 0.62 2.000 ATOM 7 OD1 ASP 109 -64.933-107.912 -77.208 -0.76 1.700 ATOM 8 OD2 ASP 109 -64.374-108.330 -75.123 -0.76 1.700 ATOM 9 H2 ASP 109 -61.633-104.125 -76.242 0.33 0.224 ATOM 10 H3 ASP 109 -60.979-105.570 -76.638 0.33 0.224 ATOM 11 H ASP 109 -61.630-104.622 -77.799 0.33 0.224 ATOM 12 HA ASP 109 -63.556-105.422 -77.489 0.10 1.320 ATOM 13 HB3 ASP 109 -62.266-107.202 -75.614 0.09 1.320 ATOM 14 HB2 ASP 109 -62.355-107.443 -77.226 0.09 1.320 ATOM 15 N TYR 110 -63.534-103.724 -75.080 -0.47 1.850 ATOM 16 CA TYR 110 -64.425-102.974 -74.191 0.07 2.275 ATOM 17 C TYR 110 -65.844-102.950 -74.766 0.51 2.000 Could anybody give me some suggestions? Another question. When I used CHARMM field, pdb2pqr recognized Mg ion, but not Ca ion. What is the atomic radius for Ca? The Mg radius given by CHARMM is 1.185, which is different than the value I googled. Thanks. Jianghai |
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From: Nathan B. <ba...@cc...> - 2007-10-24 16:13:32
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Hello -- APBS needs whitespace delimited PQR files; this file has very large negative coordinates that cause the coordinate fields to run together. If you add spaces before the "-" signs, this should fix the problem. Radii for divalent ions are very difficult to assign and extremely application-dependent. I'd suggest using hydrated radii for most implicit solvent applications. Good luck, Nathan On 10/18/07, Jianghai Zhu <jia...@um...> wrote: > Hi all, > > I generated a pqr file using pdb2pqr webserver. when I ran apbs > 0.5.1, I got the following error. > > Parsing input file I-like.pqr.in... > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from I-like.pqr. > Valist_readPQR: Error parsing ATOM field! > Error while reading molecule from I-like.pqr > Error reading molecules! > > My pqr file looks like this. > > ATOM 1 N ASP 109 -61.710-104.919 -76.847 -0.30 1.850 > ATOM 2 CA ASP 109 -63.015-105.565 -76.644 0.21 2.275 > ATOM 3 C ASP 109 -63.850-104.951 -75.482 0.51 2.000 > ATOM 4 O ASP 109 -64.777-105.570 -74.978 -0.51 1.700 > ATOM 5 CB ASP 109 -62.817-107.080 -76.428 -0.28 2.175 > ATOM 6 CG ASP 109 -64.137-107.829 -76.243 0.62 2.000 > ATOM 7 OD1 ASP 109 -64.933-107.912 -77.208 -0.76 1.700 > ATOM 8 OD2 ASP 109 -64.374-108.330 -75.123 -0.76 1.700 > ATOM 9 H2 ASP 109 -61.633-104.125 -76.242 0.33 0.224 > ATOM 10 H3 ASP 109 -60.979-105.570 -76.638 0.33 0.224 > ATOM 11 H ASP 109 -61.630-104.622 -77.799 0.33 0.224 > ATOM 12 HA ASP 109 -63.556-105.422 -77.489 0.10 1.320 > ATOM 13 HB3 ASP 109 -62.266-107.202 -75.614 0.09 1.320 > ATOM 14 HB2 ASP 109 -62.355-107.443 -77.226 0.09 1.320 > ATOM 15 N TYR 110 -63.534-103.724 -75.080 -0.47 1.850 > ATOM 16 CA TYR 110 -64.425-102.974 -74.191 0.07 2.275 > ATOM 17 C TYR 110 -65.844-102.950 -74.766 0.51 2.000 > > Could anybody give me some suggestions? > > Another question. When I used CHARMM field, pdb2pqr recognized Mg > ion, but not Ca ion. What is the atomic radius for Ca? The Mg > radius given by CHARMM is 1.185, which is different than the value I > googled. > > Thanks. > > Jianghai > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > 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/ |
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From: Nathan B. <ba...@cc...> - 2007-10-24 20:51:03
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Hello -- I'd recommend a literature search for these values since the interpretation of the data is sometimes ambiguous. Nightingale has a nice paper on some of this: TY - JOUR AB - The empirical correction to Stoke's law proposed by Robinson and Stokes has been extended for small ions to provide a concordant set of radii for the hydrated ions. Ions with a crystal ionic radius of about 2 A exhibit a minimum hydrated radius of 3.3 A corresponding to the maximum in the equivalent conductance. The internal consistency of the set of radii is demonstrated by correlation with the temperature coefficient of equivalent conductance, the viscosity B-coefficient and the partial molar ionic entropy. Except for the small monatomic ions with the minimum hydrated radius, the hydrated ionic radius at 25 is demonstrated to be a linear function of the viscosity B-coefficient. The significance of this relation is discussed in terms of the structural modification by the ions to water. N1 - Phenomenological theory of ion solvation. Effective radii of hydrated ions. AU - Nightingale, E. R. , Jr. ID - 1541 JA - Journal of Physical Chemistry NU - 9 PG - 1381-1387 BT - Phenomenological theory of ion solvation. Effective radii of hydrated ions. TY - JOUR UR - http://dx.doi.org/10.1021/j150579a011 VL - 63 PY - 1959 ER - -- Nathan On 10/24/07, Jianghai Zhu <jia...@um...> wrote: > Thanks. The space before "-" solved the problem. Another question, > what are the hydrated radii for Mg2+ and Ca2+? and where can I find > those numbers? > > Thanks again for you help. > > Jianghai > > On Oct 24, 2007, at 12:13 PM, Nathan Baker wrote: > > > Hello -- > > > > APBS needs whitespace delimited PQR files; this file has very large > > negative coordinates that cause the coordinate fields to run together. > > If you add spaces before the "-" signs, this should fix the problem. > > > > Radii for divalent ions are very difficult to assign and extremely > > application-dependent. I'd suggest using hydrated radii for most > > implicit solvent applications. > > > > Good luck, > > > > Nathan > > > > On 10/18/07, Jianghai Zhu <jia...@um...> wrote: > >> Hi all, > >> > >> I generated a pqr file using pdb2pqr webserver. when I ran apbs > >> 0.5.1, I got the following error. > >> > >> Parsing input file I-like.pqr.in... > >> Parsed input file. > >> Got PQR paths for 1 molecules > >> Reading PQR-format atom data from I-like.pqr. > >> Valist_readPQR: Error parsing ATOM field! > >> Error while reading molecule from I-like.pqr > >> Error reading molecules! > >> > >> My pqr file looks like this. > >> > >> ATOM 1 N ASP 109 -61.710-104.919 -76.847 -0.30 1.850 > >> ATOM 2 CA ASP 109 -63.015-105.565 -76.644 0.21 2.275 > >> ATOM 3 C ASP 109 -63.850-104.951 -75.482 0.51 2.000 > >> ATOM 4 O ASP 109 -64.777-105.570 -74.978 -0.51 1.700 > >> ATOM 5 CB ASP 109 -62.817-107.080 -76.428 -0.28 2.175 > >> ATOM 6 CG ASP 109 -64.137-107.829 -76.243 0.62 2.000 > >> ATOM 7 OD1 ASP 109 -64.933-107.912 -77.208 -0.76 1.700 > >> ATOM 8 OD2 ASP 109 -64.374-108.330 -75.123 -0.76 1.700 > >> ATOM 9 H2 ASP 109 -61.633-104.125 -76.242 0.33 0.224 > >> ATOM 10 H3 ASP 109 -60.979-105.570 -76.638 0.33 0.224 > >> ATOM 11 H ASP 109 -61.630-104.622 -77.799 0.33 0.224 > >> ATOM 12 HA ASP 109 -63.556-105.422 -77.489 0.10 1.320 > >> ATOM 13 HB3 ASP 109 -62.266-107.202 -75.614 0.09 1.320 > >> ATOM 14 HB2 ASP 109 -62.355-107.443 -77.226 0.09 1.320 > >> ATOM 15 N TYR 110 -63.534-103.724 -75.080 -0.47 1.850 > >> ATOM 16 CA TYR 110 -64.425-102.974 -74.191 0.07 2.275 > >> ATOM 17 C TYR 110 -65.844-102.950 -74.766 0.51 2.000 > >> > >> Could anybody give me some suggestions? > >> > >> Another question. When I used CHARMM field, pdb2pqr recognized Mg > >> ion, but not Ca ion. What is the atomic radius for Ca? The Mg > >> radius given by CHARMM is 1.185, which is different than the value I > >> googled. > >> > >> Thanks. > >> > >> Jianghai > >> > >> --------------------------------------------------------------------- > >> ---- > >> This SF.net email is sponsored by: Splunk Inc. > >> Still grepping through log files to find problems? Stop. > >> Now Search log events and configuration files using AJAX and a > >> browser. > >> Download your FREE copy of Splunk now >> http://get.splunk.com/ > >> _______________________________________________ > >> 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/ > > > > > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
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From: Jianghai Z. <jia...@um...> - 2007-10-24 21:02:31
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Thanks a lot for the reference. The hydrated radii for Mg2+ and Ca2+ are 4.28 A and 4.12 A. They are much larger than I would expect, and much larger than what CHARMM gives. Jianghai On Oct 24, 2007, at 4:51 PM, Nathan Baker wrote: > Hello -- > > I'd recommend a literature search for these values since the > interpretation of the data is sometimes ambiguous. Nightingale has a > nice paper on some of this: > > > TY - JOUR > AB - The empirical correction to Stoke's law proposed by Robinson and > Stokes has been extended for small ions to provide a concordant set of > radii for the hydrated ions. Ions with a crystal ionic radius of > about 2 A exhibit a minimum hydrated radius of 3.3 A corresponding to > the maximum in the equivalent conductance. The internal consistency > of the set of radii is demonstrated by correlation with the > temperature coefficient of equivalent conductance, the viscosity > B-coefficient and the partial molar ionic entropy. Except for the > small monatomic ions with the minimum hydrated radius, the hydrated > ionic radius at 25 is demonstrated to be a linear function of the > viscosity B-coefficient. The significance of this relation is > discussed in terms of the structural modification by the ions to > water. > N1 - Phenomenological theory of ion solvation. Effective radii of > hydrated ions. > AU - Nightingale, E. R. , Jr. > ID - 1541 > JA - Journal of Physical Chemistry > NU - 9 > PG - 1381-1387 > BT - Phenomenological theory of ion solvation. Effective radii of > hydrated ions. > TY - JOUR > UR - http://dx.doi.org/10.1021/j150579a011 > VL - 63 > PY - 1959 > ER - > > -- Nathan > > On 10/24/07, Jianghai Zhu <jia...@um...> wrote: >> Thanks. The space before "-" solved the problem. Another question, >> what are the hydrated radii for Mg2+ and Ca2+? and where can I find >> those numbers? >> >> Thanks again for you help. >> >> Jianghai >> >> On Oct 24, 2007, at 12:13 PM, Nathan Baker wrote: >> >>> Hello -- >>> >>> APBS needs whitespace delimited PQR files; this file has very large >>> negative coordinates that cause the coordinate fields to run >>> together. >>> If you add spaces before the "-" signs, this should fix the >>> problem. >>> >>> Radii for divalent ions are very difficult to assign and extremely >>> application-dependent. I'd suggest using hydrated radii for most >>> implicit solvent applications. >>> >>> Good luck, >>> >>> Nathan >>> >>> On 10/18/07, Jianghai Zhu <jia...@um...> wrote: >>>> Hi all, >>>> >>>> I generated a pqr file using pdb2pqr webserver. when I ran apbs >>>> 0.5.1, I got the following error. >>>> >>>> Parsing input file I-like.pqr.in... >>>> Parsed input file. >>>> Got PQR paths for 1 molecules >>>> Reading PQR-format atom data from I-like.pqr. >>>> Valist_readPQR: Error parsing ATOM field! >>>> Error while reading molecule from I-like.pqr >>>> Error reading molecules! >>>> >>>> My pqr file looks like this. >>>> >>>> ATOM 1 N ASP 109 -61.710-104.919 -76.847 -0.30 1.850 >>>> ATOM 2 CA ASP 109 -63.015-105.565 -76.644 0.21 2.275 >>>> ATOM 3 C ASP 109 -63.850-104.951 -75.482 0.51 2.000 >>>> ATOM 4 O ASP 109 -64.777-105.570 -74.978 -0.51 1.700 >>>> ATOM 5 CB ASP 109 -62.817-107.080 -76.428 -0.28 2.175 >>>> ATOM 6 CG ASP 109 -64.137-107.829 -76.243 0.62 2.000 >>>> ATOM 7 OD1 ASP 109 -64.933-107.912 -77.208 -0.76 1.700 >>>> ATOM 8 OD2 ASP 109 -64.374-108.330 -75.123 -0.76 1.700 >>>> ATOM 9 H2 ASP 109 -61.633-104.125 -76.242 0.33 0.224 >>>> ATOM 10 H3 ASP 109 -60.979-105.570 -76.638 0.33 0.224 >>>> ATOM 11 H ASP 109 -61.630-104.622 -77.799 0.33 0.224 >>>> ATOM 12 HA ASP 109 -63.556-105.422 -77.489 0.10 1.320 >>>> ATOM 13 HB3 ASP 109 -62.266-107.202 -75.614 0.09 1.320 >>>> ATOM 14 HB2 ASP 109 -62.355-107.443 -77.226 0.09 1.320 >>>> ATOM 15 N TYR 110 -63.534-103.724 -75.080 -0.47 1.850 >>>> ATOM 16 CA TYR 110 -64.425-102.974 -74.191 0.07 2.275 >>>> ATOM 17 C TYR 110 -65.844-102.950 -74.766 0.51 2.000 >>>> >>>> Could anybody give me some suggestions? >>>> >>>> Another question. When I used CHARMM field, pdb2pqr recognized Mg >>>> ion, but not Ca ion. What is the atomic radius for Ca? The Mg >>>> radius given by CHARMM is 1.185, which is different than the >>>> value I >>>> googled. >>>> >>>> Thanks. >>>> >>>> Jianghai >>>> >>>> ------------------------------------------------------------------- >>>> -- >>>> ---- >>>> This SF.net email is sponsored by: Splunk Inc. >>>> Still grepping through log files to find problems? Stop. >>>> Now Search log events and configuration files using AJAX and a >>>> browser. >>>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>>> _______________________________________________ >>>> 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/ >>> >>> >> >> > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > |
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