Re: [Apbs-users] Fwd: Problems in running APBS in the Gemstone
Biomolecular electrostatics software
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From: Wilfred L. <wi...@sd...> - 2008-01-29 00:16:17
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Hi, all, =20 It should be noted that the APBS calculations done through the current Gemstone interface is based on Version 0.4.0. It's accessible through the Gemstone interface using strongly typed data I/O. The strongly type data I/O support for APBS 0.5.0 is not available through Gemstone.=20 =20 The latest version of APBS 0.5.0 through the web service interface is only accessible through a client such as PMV, part of the MGLTools. =20 Cheers, =20 Wilfred =20 From: apb...@li... [mailto:apb...@li...] On Behalf Of Nathan Baker Sent: Monday, January 28, 2008 9:40 AM To: wuy...@ga... Cc: apb...@li... Subject: [Apbs-users] Fwd: Problems in running APBS in the Gemstone =20 FYI... it looks like things should be working with Gemstone now. =20 Thanks, =20 Nathan =20 Begin forwarded message: From: "bhatia karan" <ka...@sd...> Date: January 28, 2008 11:36:57 AM CST To: <sob...@gm...> Cc: <ba...@cc...>, "Wilfred Li" <wi...@sd...>, "Sriram Krishnan" <sr...@sd...> Subject: Fwd: [Apbs-users] Problems in running APBS in the Gemstone =20 =20 fyi... should be operational again... thanks for the heads up... =20 - karan =20 Begin forwarded message: From: "Sriram Krishnan" <sr...@sd...> Date: January 25, 2008 12:01:26 PM PST To: "bhatia karan" <ka...@sd...> Cc: "Wilfred Li" <wi...@sd...> Subject: Re: [Apbs-users] Problems in running APBS in the Gemstone =20 I restarted Tomcat - looks like it is working ok now. Cheers, Sriram On Jan 25, 2008, at 9:45 AM, bhatia karan wrote: thanks wilfred. this is a tomcat issue on the services end... sriram, can you take a look on the server... =20 cheers =20 - karan =20 On Jan 25, 2008, at 5:23 AM, Wilfred Li wrote: =20 FYI =20 Cheers, =20 Wilfred =20 =20 -----Original Message----- From: sob...@gm... [mailto:sob...@gm...] On Behalf Of Nathan Baker Sent: Friday, January 25, 2008 8:21 PM To: wuy...@ga... Cc: apb...@li...; Wilfred Li; Kim Baldridge; Karan Bhatia Subject: Re: [Apbs-users] Problems in running APBS in the Gemstone =20 Let me try that again with the correct e-mail addresses.... =20 On Jan 25, 2008 7:19 AM, Nathan Baker <ba...@cc...> wrote: Hello -- =20 I'm going to Cc a few folks who can hopefully help with these problems. We don't develop the Gemstone software and this sounds like a Gemstone-specific problem. =20 Thanks, =20 Nathan =20 On Jan 23, 2008, at 11:30 PM, <wuy...@ga...> <wuy...@ga... =20 wrote: =20 Hi, all =20 I am a new user of APBS and tried to run APBS in the Gemstone, but failed. The message came out as : FAILED can't open file for writing APBS input:/home/apbs_user/Software/jakarta-tomcat-5.0,30/webapps/ ROOT/apbs1200997715753/apbs.in (Too many open files). Did i miss something? I followed the instructions in the APBS tutorial (http://apbs.sourceforge.net/doc/tutorial/#id905262 ). The PQR file was generated through the on-line service at the PDB2PQR website. Part of the PQR file looks like this: ATOM 4097 N ALA 272 2.803 53.001 77.309 -0.4157 1.8240 ATOM 4098 CA ALA 272 2.914 52.314 78.565 0.0337 1.9080 ATOM 4099 CB ALA 272 1.643 51.550 78.838 -0.1825 1.9080 ATOM 4100 C ALA 272 4.128 51.391 78.592 0.5973 1.9080 ATOM 4101 O ALA 272 4.843 51.328 79.594 -0.5679 1.6612 ATOM 4102 H ALA 272 2.034 52.858 76.630 0.2719 0.6000 ATOM 4103 HA ALA 272 3.017 52.992 79.310 0.0823 1.3870 ATOM 4104 HB1 ALA 272 1.338 51.720 79.777 0.0603 1.4870 ATOM 4105 HB3 ALA 272 0.925 51.844 78.203 0.0603 1.4870 ATOM 4106 HB2 ALA 272 1.803 50.568 78.719 0.0603 1.4870 ATOM 4107 N ILE 273 4.361 50.678 77.494 -0.4157 1.8240 ATOM 4108 CA ILE 273 5.511 49.776 77.438 -0.0597 1.9080 ATOM 4109 CB ILE 273 5.329 48.758 76.302 0.1303 1.9080 ATOM 4110 CG2 ILE 273 6.518 47.766 76.233 -0.3204 1.9080 ATOM 4111 CG1 ILE 273 4.039 47.985 76.572 -0.0430 1.9080 =20 System and software are: Windows XP Professional SP2, Web browser: Firefox 2.0.2.11, Gemstone v 1.0.1 Any suggestions or solutions? Thanks =20 Walter Wu =20 =20 =09 ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. =20 =09 http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_________________ ______________________________ apbs-users mailing list apb...@li... =09 https://lists.sourceforge.net/lists/listinfo/apbs-users =20 -- Associate 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 =20 =20 =20 --=20 Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ =20 =20 =20 -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ =20 =20 =20 |