Hi, all,

 

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.

 

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.

 

Cheers,

 

Wilfred

 

From: apbs-users-bounces@lists.sourceforge.net [mailto:apbs-users-bounces@lists.sourceforge.net] On Behalf Of Nathan Baker
Sent: Monday, January 28, 2008 9:40 AM
To: wuyh0816@gate.sinica.edu.tw
Cc: apbs-users@lists.sourceforge.net
Subject: [Apbs-users] Fwd: Problems in running APBS in the Gemstone

 

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

 

 

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--

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