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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Received on Tue May 06 2014 - 05:30:03 PDT
