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
>>>>>> --
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>>>>>>
>>>>>> <1AMP_OH_sidechain.bcl>_______________________________________________
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>>>>>
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>>>>
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Received on Mon Dec 12 2011 - 13:30:04 PST
