Dear Amberists;
I was just testing some inputs for QM/MM MD for a ligand bound protein
complex. Here are some inputs for different stages of MD as well as MMGBSA.
Just for clarification of MD please let me know if these inputs are correct
or not.
Full_Mini.in
Initial minimization of QMMM: solvent molecules and added ions
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 750,
ntb = 1,
ntr = 1,
cut = 12.0,
ifqnt = 1,
/
&qmmm
qmmask= '250,238.75,86,89,75',
qmcharge=0,
qmtheory=1,
qmshake=1,
qm_ewald=1,
qm_pme=1,
/
Hold the Protein fixed
10.0
RES 1 557
Heating.in
*Heating Step of QMMM: stage-2 &cntrl imin= 0, irest=0, NTX=1, ntb=
1, NTPR=500, NTWX=500, NTWR=500, ntr=1, Tempi=0.0, Temp0=300.0,
ifqnt=1, NTT=3, gamma_ln=1.0, NTC=2, NTF=2, cut= 12.0,
nstlim=2500, dt=0.002,/&qmmmqmmask=
'250,238.75,86,89,75',qmcharge=0,qmtheory=1,qmshake=1,qm_ewald=1,qm_pme=1,/Keep
Protein and inhibitor fixed with weak restraints10.0RES 1 557ENDEND*
equil.in
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=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,
ifqnt=1,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=250000,
dt=0.002
/
&qmmm
qmmask= '250,238.75,86,89,75',
qmcharge=0,
qmtheory=1,
qmshake=1,
qm_ewald=1,
qm_pme=1,
/
*md.in <
http://md.in>*
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=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,
ifqnt=1,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=2500000,
dt=0.002
/
&qmmm
qmmask= '250,238.75,86,89,75',
qmcharge=0,
qmtheory=1,
qmshake=1,
qm_ewald=1,
qm_pme=1,
/
*MMGBSA script*
Input file for running PB and GB in serial
&general
startframe=1, endframe=5000, interval=5verbose=2,entropy=1,keep_file=0,
/
&gb
igb=5,saltcon=0.15,ifqnt=1,qmmask= '250,238.75,86,89,75',
qmcharge=0,qmtheory=1,
/
Please confirm once if these scripts are well to perform QM/MM MD at PM3
level and calculate post MD QM/MM MMGBSA.
Thanks a lot in advance
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun May 11 2014 - 13:00:02 PDT
