Re: [AMBER] MCPB execution error

From: Ben Roberts <ben.roberts.geek.nz>
Date: Sun, 11 Dec 2011 23:17:10 -0500

I apologise for the blank email I just sent. I meant to say that we are working on putting a patch together that may fix the problem you're encountering. It's not one we've seen before, though. For which reason it's unlikely the fix will be quick or easy. You hadn't heard from us yet because we had nothing new to tell you.

Incidentally, what operating system and C++ compiler did you use?

Regards,
Ben

-- 
For greater security, I support S/MIME encryption.
On 11/12/2011, at 11:05 PM, "Soma Ghosh" <soma.mbu.iisc.ernet.in> wrote:
> Dear Sir,
> 
> I am resending the mail as a gentle reminder. Sorry, if I have caused an
> inconvenience.
> 
> Regards
> Soma
>> Dear Sir,
>> 
>> 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.
>> 
>> Thanks and Regards
>> Soma Ghosh
>> 
>>> Dear Soma,
>>> 
>>> Are you using the latest code within AmberTools 1.5 from
>>> http://ambermd.org/AmberTools-get.html ?
>>> 
>>> What did you change in the 1AMP_OH_sidechain.bcl file?
>>> 
>>> Regards,
>>> Martin
>>> 
>>> 
>>> On 28 Nov 2011, at 06:01, Soma Ghosh wrote:
>>> 
>>>> Dear AmberUsers,
>>>> 
>>>> I am trying to build the parameter files for an amino-acid metal complex. To
>>>> build the parameters, i am using MCPB as suggested in an earlier mail. The
>>>> tool
>>>> seems to have installed properly. However, I encounter an error when i run
>>>> the
>>>> following command (using the example scripts provided in the data folder)
>>>> 
>>>>> MCPB -i 1AMP_OH_sidechain.bcl -l 1AMP_OH_sidechain.bcl.log
>>>> 
>>>> I get the following error :
>>>> 
>>>> terminate called after throwing an instance of 'std::logic_error'
>>>> what():  basic_string::_S_construct NULL not valid
>>>> Aborted
>>>> 
>>>> I suppose it has something to do with the boost library. Could some one
>>>> please
>>>> suggest me some solutions. I am attaching the 1AMP_OH_sidechain.bcl file
>>>> (however, it is the same as provided in the data folder)
>>>> 
>>>> Thanks and Regards
>>>> Soma Ghosh
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>>>> 
>>>> <1AMP_OH_sidechain.bcl>_______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> 
>>> 
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>>> 
>> 
>> 
>> 
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>> 
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>> 
> 
> 
> 
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Received on Sun Dec 11 2011 - 20:30:03 PST
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