Hi Saugata,
it looks like a problem in the definition of your .prmtop files. I've
experienced similar errors (even the segmentation fault you mentioned
earlier with Amber11 calculation) due to an incorrect definition of
masks in the input file or unconsistencies with the complex, ligand or
receptor definitions between the mmpbsa.in and prmtops. I suggest you to
carefully check your prmtops, in particular ba2291_prot.prmtop as
evidenced by the attached log.
Regards
Alessandro
Il 20/02/2013 09:08, Saugata Hazra ha scritto:
> Hi All,
>
> After getting suggestions from you I have upgraded my AmberTools from
> AmberTools 1.5 to AmberTools12. But even after doing that I'm getting
> another error message different from the earlier. I have copied both the
> error messages. it would be great if you would have suggestions regarding
> further proceedings.
>
> *Error message ** After Upgradation : (When I have Amber 11 with
> AmberTools 12)*
> saugata.saugata:~$ cd Desktop/ba2291/mdrun/ba2291_atp
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O
> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> bash: /home/saugata/amber12/bin/MMPBSA: No such file or directory
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA.py
> -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /home/saugata/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /home/saugata/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with /home/saugata/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> mmpbsa_py_energy: malloc.c:3801: _int_malloc: Assertion `(unsigned
> long)(size) >= (unsigned long)(nb)' failed.
> CalcError: /home/saugata/amber12/bin/mmpbsa_py_energy failed with prmtop
> ba2291_prot.prmtop!
> Exiting. All files have been retained.
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
>
>
> *Error message Before Upgradation: (When I had Amber 11 with AmberTools 1.5)
> *
> saugata.saugata:~/Desktop/
> ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp ba2291_com.prmtop -rp
> ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/saugata/amber11/bin/ptraj
> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> for GB calculations
> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> for PB calculations
> Preparing trajectories for simulation...
> 50 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> calculating receptor contribution...
> Segmentation fault (core dumped)
> Error: mmpbsa_py_energy error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA.py --clean
> MMPBSA.py: command not found
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA --clean
> Reading command-line arguments and input files...
> Cleaning temporary files
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
>
> Thanks,
> Saugata
>
>
>
>
>
> On Tue, Feb 19, 2013 at 9:43 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Tue, Feb 19, 2013 at 9:31 AM, Saugata Hazra <saugata.iitk.gmail.com
>>> wrote:
>>> Thank you very much Jason.
>>> One more question to make it sure.
>>> As I have mentioned earlier, that I have Amber 11 & AmberTools 1.5.
>>> So, is it enough to upgrade only the AmberTool or I also have to upgrade
>> my
>>> AMBER to AMBER12.
>>>
>> Upgrading AmberTools is sufficient for MMPBSA.py.
>>
>>
>>> Thanks,
>>> Saugata
>>>
>>> On Tue, Feb 19, 2013 at 9:00 AM, Jason Swails <jason.swails.gmail.com
>>>> wrote:
>>>> On Tue, Feb 19, 2013 at 8:02 AM, Saugata Hazra <saugata.iitk.gmail.com
>>>>> wrote:
>>>>> Hi,
>>>>>
>>>>> I am running a binding energy calculation (MM-PBSA) for
>> protein-ligand
>>>>> complex using Amber11 and AmberTools 1.5. I am following Ross Walker
>>>>> tutorial but have got error message during MMPBSA calculation as
>>> follows:
>>>>> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
>>> $AMBERHOME/bin/MMPBSA
>>>>> -O
>>>>> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop
>> -cp
>>>>> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
>>>>> Reading command-line arguments and input files...
>>>>> Loading and checking parameter files for compatibility...
>>>>> ptraj found! Using /home/saugata/amber11/bin/ptraj
>>>>> mmpbsa_py_energy found! Using
>>> /home/saugata/amber11/bin/mmpbsa_py_energy
>>>>> for GB calculations
>>>>> mmpbsa_py_energy found! Using
>>> /home/saugata/amber11/bin/mmpbsa_py_energy
>>>>> for PB calculations
>>>>> Preparing trajectories for simulation...
>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>
>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>> calculating complex contribution...
>>>>> calculating receptor contribution...
>>>>> Segmentation fault (core dumped)
>>>>>
>>>> Yikes. A segfault from NAB. Try upgrading to AmberTools 12 and use
>> that
>>>> version instead. You can also try putting "use_sander=1" in the
>> &general
>>>> section of the MMPBSA.py input file to force it to use sander instead.
>>>>
>>>> Good luck,
>>>> Jason
>>>>
>>>> --
>>>> Jason M. Swails
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Candidate
>>>> 352-392-4032
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>>
>>> *Know me Know fun, no me no fun!!!*
>>> Dr. Saugata Hazra
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
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Received on Wed Feb 20 2013 - 01:00:02 PST
