I have some doubts about your input as you are running 10ns you can easily
calculate it by taking average frames from starting to last. At a
particular frame if you want to calculate on the frame by frame basis then
it should go well. For a better binding free energy approximation you
should calculate at certain(at each nanoseconds, say for example binding
free at 1ns, 2ns, 3ns, 4ns and ... then check the convergence) intervals
and make a plot to check convergence. Individual frame or average frame is
not a good way if you want to do a proper work.
Though here is a script which might help you in running both MD and MMGBSA
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=0,
ig=-1
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=5000000,
dt=0.002
/
Input file for running PB and GB in serial
&general
startframe=1, endframe=10000, interval=10,keep_file=0, verbose=1,
entropy=1,
/
&gb
igb=5,saltcon=0.15,
/
&decomp
idecomp=1,
print_res="557;82;175;216;93;221;214;222;223;224;90;305;89;176;166;167;177;88;87;168",
dec_verbose=1,csv_format=0,
/
On Tue, May 6, 2014 at 2:15 PM, 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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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue May 06 2014 - 08:30:05 PDT
