Re: [AMBER] MCPB execution error

From: Soma Ghosh <soma.mbu.iisc.ernet.in>
Date: Wed, 7 Dec 2011 11:53:31 +0530 (IST)

Dear Sir,

Please find the information below:

> 1. The operating system you're using when running MTK++
32 bit Ubuntu 10.04 LTS

> 2. Whether you compiled on the same computer that you're attempting to run on
(likely, but not guaranteed, especially if it's a cluster)
yes. I compiled MTK++ on the same computer

> 4. The compilers (name and version) you used to build MTK++
gcc version 4.4.3 (no variables were provided while running the configure
command. So, it must have identified the compiler by itself. The config.status
file mentions the gcc compiler)

> 5. The name of the XML parser you used when building MTK++ (tinyXML is the
default, but you may have used Xerces or QT), or, if you don't know how to
ascertain this, the config.h file in $AMBERHOME/AmberTools/src/mtkpp
tinyXML was used

> 5. The exact commands you used on the command line when running MTK++, leading
up to the step during which the crash occurred
(After copying the required files in a separate folder the following commands
were executed)

1. > sh genMetalFF.sh -n 1AMP_OH (this creates a number of file. One of them
being : 1AMP_OH_addHs.bcl)
2. > MCPB -i 1AMP_OH_addHs.bcl -l 1AMP_OH_addHs.bcl.log
3. > MCPB -i 1AMP_OH_sidechain.bcl -l 1AMP_OH_sidechain.bcl.log
(1AMP_OH_sidechain.bcl file copied form the
$AMBER/AMBERHOME/examples/mtkpp/MCPB/data folder)
The above command throws the following error:
terminate called after throwing an instance of 'std::logic_error'
  what(): basic_string::_S_construct NULL not valid
Aborted
I checked the 1AMP_OH_sidechain.bcl file. It requires 1AMP_OH_fixed.pdb as an
input and the same is present in the working directory. I also replaced 'NAME'
by '1AMP_OH' in the 1AMP_OH_sidechain.bcl file and tried to run the script. It
throws the same error.

> 6. The log file produced by the step on which MTK++ bombs out, if any, with
particular attention to any warnings or errors reported in the log
I am attaching the log file. It does not say anything specific about the
termination. Just writes the list of commands that has to be executed as
provided in the input file.

> 7. Indications, if any, of source code files and their line numbers that are
giving rise to this problem
No such indications have been made. except the error on the terminal.

I hope the informations provided are useful. Apart from the
1AMP_OH_sidechain.bcl.log file, I am also attaching the config.log status. It
may be required to check if the installation is done properly.

Thanks and Regards
Soma Ghosh
> Hi Soma,
>
> On 6/12/2011, at 12:31 a.m., Soma Ghosh wrote:
>
>> Dear Sir,
>>
>> I am resending the e-mail as I am not sure if you have received it.
>> I have used the latest AmberTools. I reinstalled the complete thing again to
>> be
>> sure. Also, I have made no changes to the 1AMP_OH_sidechain.bcl. This file is
>> generated after running the following command:
>>
>>> sh genMetalFF.sh -n 1AMP_OH
>>
>> and the sh script is the same as available in the
>> $AMBERHOME/AmberTools/examples/mtkpp/MCPB directory.
>
> Would you be so kind as to supply us with the following information:
>
> 1. The operating system you're using when running MTK++
> 2. Whether you compiled on the same computer that you're attempting to run on
> (likely, but not guaranteed, especially if it's a cluster)
> 3. If not, the operating system you used when compiling MTK++
> 4. The compilers (name and version) you used to build MTK++
> 5. The name of the XML parser you used when building MTK++ (tinyXML is the
> default, but you may have used Xerces or QT), or, if you don't know how to
> ascertain this, the config.h file in $AMBERHOME/AmberTools/src/mtkpp
> 5. The exact commands you used on the command line when running MTK++, leading
> up to the step during which the crash occurred
> 6. The log file produced by the step on which MTK++ bombs out, if any, with
> particular attention to any warnings or errors reported in the log
> 7. Indications, if any, of source code files and their line numbers that are
> giving rise to this problem
>
> Thanks,
> Ben_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Tue Dec 06 2011 - 22:30:02 PST
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