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
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Received on Thu Feb 20 2014 - 11:00:04 PST
