Thank you Dr. Vlad.
As i have done my simulation with amber 11 i want to calculate binding
energy with MMPBSA from Ambertools1.5, is there any way to calculate
binding energy to all frames as like -eo option in new MMPBSA.
Regards
On 2014-02-21 18:11, Vlad Cojocaru wrote:
> We and others did lots of tests with different MMPBSA parameters and the
> result is that parameters can influence the dG even by 100 kcal/mol ...
> In your case, the difference comes probably because the older MMPBSA
> used different default values for certain parameters ...
>
> The other issue is that the "best" combination of parmeters seem to
> depend quite a bit on the system under study. This makes the choices for
> the defaults very tricky ....
>
> Short answer, nobody but yourself after very careful investigation will
> probably be able to tell you which of your result is "good" and which
> one is "bad" ...
>
> Longer answer ...
>
> My advice is to understand and test very carefully all parameters used
> by MMPBSA and read as much literature with MMPBSA studies as possible
> ... Ideally you have a toy system for which you have some experimental
> data that has similar properties with your system. You can then use this
> toy system to test which combination of parameters is best for your case
> .... The other important thing, use your knowledge and physico-chemical
> intuition to understand whether a result is potentially reasnable or is
> non-sense ...
>
> MMPBSA can be a very useful technique but is very tricky ....
>
> Good luck,
> Vlad
>
> On 02/21/2014 12:56 PM, Arun Kumar Somavarapu wrote:
> Thanks all for your valuable information. As like Dr. Jason said i changed the environment variables to AmberTools 13 and it got worked out. Thanks Dr. Vlad I got the result in the way i was expecting with -eo option, but there was a huge difference in POISSON BOLTZMANN Avg binding energy say -35 with old version and 42 with Ambertools 13, where as not the case with GENERALIZED BORN, which one i have to consider and why is that difference occurred only in case of Poisson Boltzmann? Regards On 2014-02-21 00:12, Vlad Cojocaru wrote: Hi Arun, Sorry, I overlooked one phrase in your error message (the most important one) ... "getpdb: can't open file pdb" ... I have never seen this error before. I guess somebody else can help more ... When I mentioned about the memory issue, I referred to the error "failed with prmtop" Vlad On 02/20/2014 05:55 PM, Arun Kumar Somavarapu wrote: yes Sir, the -eo option is present in AmberTools 13 and i was using Amber 11 and AmberTools 12 where -eo option
is not present. later on i tried MMPBSA.py in AmberTools 13 with command like MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ../complex-solv.prmtop -cp ../complex-gas.prmtop -rp ../receptor-gas.prmtop -lp ../ligand-gas.prmtop -y ../prod1.mdcrd.gz -eo energyout this time it is exiting with an error as fallows Loading and checking parameter files for compatibility... mmpbsa_py_energy found! Using /home/braf/md/amber11/bin/mmpbsa_py_energy cpptraj found! Using /home/braf/md/amber11/bin/cpptraj Preparing trajectories for simulation... 50 frames were processed by cpptraj for use in calculation. Running calculations on normal system... Beginning GB calculations with /home/braf/md/amber11/bin/mmpbsa_py_energy calculating complex contribution... getpdb: can't open file pdb CalcError: /home/braf/md/amber11/bin/mmpbsa_py_energy failed with prmtop ../complex-gas.prmtop! Exiting. All files have been retained. can you please help me to resolve this. Thanking you. On 2014-02-20 18:09,
Vlad Cojocaru wrote: No, it is not. Please check the AmberTools 13 user guide. The "-eo" option is described very clear in the section describing how to run MMPBSA.py. Best wishes Vlad On 02/20/2014 12:45 PM, Arun Kumar Somavarapu wrote: Hello Sir, Thanks for reply. I am not able to find option -eo. There is an option of -do (decomp_output_file), is that you are talking about? Regards On 2014-02-20 16:48, Vlad Cojocaru wrote: Please check the "-eo" option when running MMPBSA.py ... This outputs a file with energies at every processed frame. Best Vlad On 02/20/2014 12:12 PM, Arun Kumar Somavarapu wrote: Hello Sir, I am calculating free energy of a protein ligand complex and want to see the binding energy variation in each frame through out time scale. After sing MMPBSA.py I am able to see only one value for Delta G binding energy in FINAL_RESULTS_MMPBSA.dat file. I have also checked MMPBSA_complex_pb.mdout where individual energies are present to each trj frame, will these be further
processed to get final binding energy for each frame? or else, if there is any other method please guide me. Thanking you. Regards
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru [1]
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--
Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
Links:
------
[1] http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
[2] http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Feb 24 2014 - 05:30:05 PST
