Dear Sir,
Yes it works. Incidentally my AMBERHOME was set to amber9 folder (amber 9 is
installed in the machine) and MCPB package came inside amber11 folder. I changed
AMBERHOME to amber11 and it worked. Sorry, for the inconvenience. Should have
been more careful.
Thanks and Regards
Soma Ghosh
> Hi Soma,
>
> This is a long shot but did you set AMBERHOME correctly before running MCPB?
>
> Cheers,
> Martin
>
> On 12 Dec 2011, at 04:54, Soma Ghosh wrote:
>
>> Dear Sir,
>>
>> Thank you for the quick reply. I can surely wait, just wanted to be sure that
>> you have received my reply.
>>
>> My operating system is : 32 bit Ubuntu 10.04 LTS and my c++ compilers is c++
>> (Ubuntu 4.4.3-4ubuntu5) 4.4.3.
>>
>> I would be glad to be of any help to you. Please inform me if any other
>> details
>> are also required.
>>
>> Thanks and Regards
>> Soma Ghosh
>>> 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
>>>>>>> --
>>>>>>> This message has been scanned for viruses and
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>>>>>>> believed to be clean.
>>>>>>>
>>>>>>> <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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>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
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>>
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Received on Mon Dec 12 2011 - 20:00:02 PST
