some update:
I've noticed that the above error takes place when I used both
trajectories provided in the -y for the mmgbsa (here the second
trajectory has been stripped from different system initially consisted
of different number solvent molecules. However both stripped
topologies (obtained for each trajectories) consists of the same
number of atoms so I have no idea why such error take place.
James
2015-03-16 14:00 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> Hi Bill,
>
> just faced with the error of the post-processing of such trajectories
> and topologiest
>
> 1) here I'm using ante-MMPBSA.py just to create three input topologies
> for mmgbsa.py providing already stripped topology (only protein and
> ligand).
>
> ante-MMPBSA.py -p ${sim}/strip.protein.parm7 -c complex.prmtop -r
> receptor.prmtop -l ligand.prmtop -n :MOL
>
>
> 2) then I use three generated prmtops (here I checked it according to
> the number of atoms in each- all should be correct for first instance)
> as well as 2 stripped trajectories as the inputs for the mmgbsa:
> nmpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> mmgbsa_nm_${simulation}.dat -sp ${sim}/strip.protein.parm7 -cp
> ${sim}/strip.protein.parm7 -rp receptor.prmtop -y
> ${sim}/merged_md1_2.nc ${sim}/striped_md3.nc -lp ligand.prmtop >
> progress.log 2>&1" > ./mmgbsa_${simulation}.pbs
>
> 3) having input file for the decomposition
>
> &general
> startframe= 1, interval=50, keep_files=2, netcdf=1
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &decomp
> idecomp=1, csv_format=0, dec_verbose=0,
>
>
> the calculation is begining- so there is no problems with any of
> inputs- but occasionally I've obtained error
>
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13
> CalcError: /home/cmoon/Prog/amber12/bin/cpptraj failed with prmtop
> /home/cmoon/total_decomp/5p3_carvone/strip.protein.parm7!
> Error occured on rank 14.
>
> How it could be fixed most trivially?
>
>
> James
>
> 2015-03-05 13:44 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
>> Personally, I use tleap to generate all prmtops necessary for MMPBSA.py calculations prior to running any simulation. But if you have already started running simulations, I would advise using ante-MMPBSA.py
>>
>> -Bill
>>
>> On Mar 5, 2015, at 6:39 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>
>>> so in simplest case only 2 inputs should be provided : stripped
>>> merged trajectory as well as stripped topology for each system
>>> shouldn't it? BTW is it possible to use ante-mmpbsa to strip common
>>> mask from several input trajectories consisted of different number of
>>> solvent (so its number of atoms will be also different) or it will
>>> better anyway to use tleap?
>>>
>>> James
>>>
>>> 2015-03-05 11:45 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
>>>> Thanks alot!
>>>>
>>>> James
>>>>
>>>> 2015-03-04 16:38 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
>>>>> For MMPBSA.py calculations, explicit solvent molecules are never used for
>>>>> the calculation. MMPBSA.py removes the solvent before doing any
>>>>> calculations. So if you give it a trajectory (or multiple trajectories)
>>>>> without water molecules along with a dry/stripped topology, the calculation
>>>>> will be the same, but MMPBSA.py just won't have to remove the water atoms
>>>>> first.
>>>>>
>>>>> In this case, you do not need to specify anything for the strip mask. If
>>>>> you don't give MMPBSA.py a solvated topology file, it knows not to strip
>>>>> any residues from the trajectory.
>>>>>
>>>>> You can use the startframe variable in the &general namelist to specify
>>>>> what frame you want the calculation to start on. And I believe that is for
>>>>> each trajectory if you provide more than one.
>>>>>
>>>>> -Bill
>>>>>
>>>>> On Wed, Mar 4, 2015 at 9:48 AM, James Starlight <jmsstarlight.gmail.com>
>>>>> wrote:
>>>>>
>>>>>> and some additional questions:
>>>>>>
>>>>>> 1- what should be provided in the mmgbsa.input file for the stripped
>>>>>> mask in case when I use already stripped from the solvent trajectories
>>>>>> 2- how it possible not to take into the analysis x fist snapshots from
>>>>>> each processed trajectory used within one mmgbsa calculation?
>>>>>>
>>>>>> James
>>>>>>
>>>>>> 2015-03-04 15:10 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
>>>>>>> Hi Bill,
>>>>>>>
>>>>>>> so I'd like to specify more:
>>>>>>> mmgbsa.py accept *several* input trajectories files (specified after
>>>>>>> its -y flag) each of which should consist only of the atoms for ligand
>>>>>>> and receptor as well as stripped topology with the same atoms isn't
>>>>>>> it? so for calculation of the free energy of binding and its
>>>>>>> decomposition the presence of solvent within the system is not needed?
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> James
>>>>>>>
>>>>>>> 2015-03-03 16:23 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
>>>>>>>> You will need to strip all the water molecules out of the trajectories
>>>>>>>> using cpptraj prior to running MMPBSA.py since they all have different
>>>>>>>> numbers of water molecules, and then use the dry prmtop and just don't
>>>>>>>> provide a solvated prmtop. You don't have to merge them all into one
>>>>>>>> trajectory using cpptraj prior to running MMPBSA.py. You can just use a
>>>>>>>> wild card or just list them all after the -y flag in the MMPBSA.py
>>>>>> command.
>>>>>>>>
>>>>>>>> I hope that helps.
>>>>>>>>
>>>>>>>> -Bill
>>>>>>>>
>>>>>>>> On Tue, Mar 3, 2015 at 6:58 AM, James Starlight <jmsstarlight.gmail.com
>>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Dear Amber users!
>>>>>>>>>
>>>>>>>>> I'm going to perform per-residue decomposition analysis for several
>>>>>>>>> protein-ligand systems having 3 independent trajectories for each
>>>>>>>>> system. I wounded to know
>>>>>>>>> 1) is it possible to include several trajectories tax the standard
>>>>>>>>> input to MMPBSA.py or alternatively I should to merge all trajectories
>>>>>>>>> for the same system together using cpptraj?
>>>>>>>>> 2) what I should do if some of the trajectories for the same system
>>>>>>>>> are consisted of different number of atoms (and its parm7 files also
>>>>>>>>> differs)-> because each time each system has been solvated de novo->
>>>>>>>>> so the number of solvent molecules in identical protein-ligand systems
>>>>>>>>> are differs. In these regards Is it possible to i) strip all solvent
>>>>>>>>> using cpptraj from each trajectory and ii) to join all of them
>>>>>>>>> together ( consisted of only protein-ligand atoms) iii) to provide
>>>>>>>>> stripped parm7 file for the MMPBSA.py as well as the stripped
>>>>>>>>> trajectory.
>>>>>>>>>
>>>>>>>>> I would be very thankful for any other solutions,
>>>>>>>>>
>>>>>>>>> James
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Bill Miller III
>>>>>>>> Post-doc
>>>>>>>> University of Richmond
>>>>>>>> 417-549-0952
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Bill Miller III
>>>>> Post-doc
>>>>> University of Richmond
>>>>> 417-549-0952
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Mon Mar 16 2015 - 07:00:03 PDT
