Please send us the relevant input file.

 

Note that, when output files are created, that scanf error message can often be ignored.

 

Thank you,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Ooker [mailto:ganuongphap@gmail.com]
Sent: Wednesday, May 21, 2014 1:08 AM
To: Baker, Nathan; apbs-users@lists.sourceforge.net
Subject: Re: [apbs-users] asc_getToken: Error occurred (bailing out).

 

I have tried to use the input from APBS web site, the error is still there (although output files are created). When using apbs input, the output is:

Parsing input file input...

Parsed input file.

Got paths for 3 molecules

Reading PQR-format atom data from model_outNB.pqr.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

998 atoms

Centered at (1.382e+01, 5.283e+00, 8.258e+00)

Net charge -1.40e+01 e

Reading PQR-format atom data from model_outNpep.pqr.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

379 atoms

Centered at (1.753e+01, -1.723e+00, 1.470e+01)

Net charge 4.00e+00 e

Reading PQR-format atom data from model_outBoxB19.pqr.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

619 atoms

Centered at (1.306e+01, 7.586e+00, 4.177e+00)

Net charge -1.80e+01 e

Preparing to run 6 PBE calculations.

 

When using apbs input > log, the log file report no error but the terminal appear:

 

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

Warning: The 'energy' print keyword is deprecated.

Use elecEnergy for electrostatics energy calcs.

 

Can you explain this? Thank you.

--

Ooker.


On Tuesday 20 May 2014 14:18:26 you wrote:

Hello –

 

That input should not work because there is no calculation:  you need to add an APOLAR or ELEC block to your input file.

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Ooker [mailto:ganuongphap@gmail.com]
Sent: Sunday, May 18, 2014 5:34 PM
To: Baker, Nathan
Subject: Re: [apbs-users] asc_getToken: Error occurred (bailing out).

 

Hi Nathan,

 

Here are my input and PQR files.

 

--

Ooker.


On Monday 19 May 2014 01:03:29 you wrote:

Hello –

 

Can you please send the entire input and PQR file?

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Ooker [mailto:ganuongphap@gmail.com]
Sent: Sunday, May 18, 2014 9:57 AM
To:
apbs-users@lists.sourceforge.net
Subject: [apbs-users] asc_getToken: Error occurred (bailing out).

 

Hi,

When I tried to use this file named input (test is a pqr file already)

 

read

mol pqr test

end

 

by this command

 

apbs input

 

I meet this error

 

Parsing input file input...

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

Parsed input file.

Got paths for 1 molecules

Reading PQR-format atom data from test.

asc_getToken: Error occurred (bailing out).

Vio_scanf: Format problem with input.

998 atoms

Centered at (1.382e+01, 5.283e+00, 8.258e+00)

Net charge -1.40e+01 e

Preparing to run 0 PBE calculations.

----------------------------------------

CLEANING UP AND SHUTTING DOWN...

Destroying force arrays.

No energy arrays to destroy.

Destroying multigrid structures.

Destroying 1 molecules

Final memory usage: 0.000 MB total, 0.667 MB high water

 

I have searched I found this similar problem in this link: http://sourceforge.net/p/apbs/mailman/message/4605762/, but the link Nathan gave has no longer existed.

 

Thank you.

--

Ooker.