Hi, I never worked with ions as part of the ligand, but I did defining
them as part of the receptor (eg Mg ions in GTPases). You could try
this, even if I guess it should also be possible to specify a mask
including the ion within ligand atoms.
Regards
Alessandro
Inviato da iPhone
Il giorno 24/feb/2013, alle ore 01.51, Saugata Hazra <saugata.iitk.gmail.com
> ha scritto:
> Thank you very much Alessandro for your reply. I guess you are right
> regarding this prmtop problem.
> The problem arises probably because of the fact that I had a metal
> (Mn2+)
> included with the protein.
> Now after taking out the metal, the ba2291_prot.prmtop file is finally
> running.
>
> But now I have to treat Mn2+ as a ligand, so I have two ligands
> ( one is
> ATP and another is Mn2+ ion). There is option of only one ligand and a
> merged file including both is not running.
> Any further suggestion!!!!!!!!!!!!
>
> Saugata
>
> On Wed, Feb 20, 2013 at 3:50 AM, Alessandro Contini <
> alessandro.contini.unimi.it> wrote:
>
>> 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<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<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<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
>>
>>
>
>
> --
>
> *Know me Know fun, no me no fun!!!*
> Dr. Saugata Hazra
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Feb 24 2013 - 01:00:03 PST
