FYI... it looks like things should be working with Gemstone now.

Thanks,

Nathan

Begin forwarded message:

From: "bhatia karan" <karan@sdsc.edu>
Date: January 28, 2008 11:36:57 AM CST
To: <sobolevnrm@gmail.com>
Cc: <baker@ccb.wustl.edu>, "Wilfred Li" <wilfred@sdsc.edu>, "Sriram Krishnan" <sriram@sdsc.edu>
Subject: Fwd: [Apbs-users] Problems in running APBS in the Gemstone


fyi... should be operational again... thanks for the heads up...

- karan

Begin forwarded message:

From: "Sriram Krishnan" <sriram@sdsc.edu>
Date: January 25, 2008 12:01:26 PM PST
To: "bhatia karan" <karan@sdsc.edu>
Cc: "Wilfred Li" <wilfred@sdsc.edu>
Subject: Re: [Apbs-users] Problems in running APBS in the Gemstone

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...

cheers

- karan

On Jan 25, 2008, at 5:23 AM, Wilfred Li wrote:

FYI

Cheers,

Wilfred


-----Original Message-----
From: sobolevnrm@gmail.com [mailto:sobolevnrm@gmail.com] On Behalf Of
Nathan Baker
Sent: Friday, January 25, 2008 8:21 PM
To: wuyh0816@gate.sinica.edu.tw
Cc: apbs-users@lists.sourceforge.net; Wilfred Li; Kim Baldridge; Karan
Bhatia
Subject: Re: [Apbs-users] Problems in running APBS in the Gemstone

Let me try that again with the correct e-mail addresses....

On Jan 25, 2008 7:19 AM, Nathan Baker <baker@ccb.wustl.edu> wrote:
Hello --

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.

Thanks,

Nathan

On Jan 23, 2008, at 11:30 PM, <wuyh0816@gate.sinica.edu.tw>
<wuyh0816@gate.sinica.edu.tw

wrote:

Hi, all

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

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

Walter Wu


------------------------------------------------------------------------
-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.

http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_________________
______________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
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/



--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis