Were there 501 frames in the original trajectory? Because in your input
file you specify for the analysis to start at frame 500 (start_frame=500).
If there were 500 frames, then MMPBSA.py would have analyzed frame 500 and
frame 501, a total of two frames.
That's my guess.
-Bill
On Tue, May 6, 2014 at 8:15 AM, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> Dear amber users,
>
> I ran a simulation of 10ns with following parameters
>
> Molecular dynamic simulation for 10ns
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> ntpr=5000,
> ntwr=50000,
> ntwx=5000,
> ioutfm=1,
> ntxo=2,
> nstlim=5000000,
> dt=0.002,
> ntt=1,
> tautp=10.0,
> temp0=310.0,
> ntp=1,
> pres0=1,
> ntc=2,
> ntf=2,
> ntb=2,
> cut=8.0,
> /
>
> If I am correct the number of frames (snapshots) are nstlim/ ntwx
> =5000000/5000=1000
>
> Now I calculated binding free energy and something in the output confused
> me. It says Calculations performed using 2 complex frames BUT as I have not
> mentioned interval variable. whose default value is 1, the total frames
> should have been 501. Am I wrong ? by the way I am using AMBER12
>
> Input file:
> |--------------------------------------------------------------
> |Input file for running GB
> |&general
> | startframe=500, verbose=1,entropy=1,
> |/
> |&gb
> | igb=2, qm_theory = 'PM3', saltcon=0.100
> |/
> |&decomp
> | idecomp=2, dec_verbose= 2
> |/
> |--------------------------------------------------------------
> |MMPBSA.py Version=13.0
> |Solvated complex topology file: complex_solvated_noIons.prmtop
> |Complex topology file: complex.prmtop
> |Receptor topology file: receptor.prmtop
> |Ligand topology file: ligand.prmtop
> |Initial mdcrd(s): 5md_b_strip.mdcrd
> |
> |Receptor mask: ":1-154"
> |Ligand mask: ":155"
> |Ligand residue name is "UNK"
> |
> |Calculations performed using 2 complex frames.
> |
> |Generalized Born ESURF calculated using 'LCPO' surface areas
> |
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mol (Temperature is 298.15 K).
>
>
> I hope someone can clear my doubt.
>
> Thanks and regards,
> Nitin Sharma
> Department of Pharmacy,Faculty of Science,National University of
> Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543, Republic
> of Singapore: sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ;
> Phone +6582969643; http://www.linkedin.com/in/imsharmanitin
>
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>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Tue May 06 2014 - 08:00:04 PDT
