122
cut=10.0, ntb=2, pres0=1.0, ntp=1, taup=2.0,
ntr=0,
ntc=2, ntf=2,
tempi=310.0, temp0=310.0,
ntt=3, gamma_ln=2.0,
nstlim=1500000000, dt=0.002,
/end
7. Input files for MM–PBSA enthalpy and entropy calculations:
mmpbsa_enthalpy.in
Input file for running PB and GB
&general
endframe=1000, startframe=1, interval=10,Calculate from
trajectory frame 1 to 1000 every 10
/
&gb Perform MM–GBSA calculation
igb=5, Use a modified GB model[31]
saltcon=0.100 Salt concentration (in M)
/
&pb Perform MM–PBSA calculation
istrng=0.100, Ionic strength (in M)
/
mmpbsa_entropy.in
Input file for running entropy calculations using NMode
&general
endframe=1000,
/
&nmode Perform normal mode analysis
nmstartframe=100, nmendframe=1000, nminterval=10,
nmode_igb=1, Default GB model [32]
nmode_istrng=0.1, Ionic strength (in M)
/
8. Example of a simple input file for conformational analysis with
cpptraj:
ptraj.in
trajin complex_md.nc Read and analyze each
frame of MD trajectory
distance :2@O1 :3@H2 out distance_2- 3_complex.
out Calculate the distance between oxygen atom
labeled O1 in residue 2 and hydrogen atom labeled H2 in residue 3. Report the results for
every frame in output file named distance_2-3_
complex.out
rms first mass out rms_CD.out :1-14 Calculate
RMSD for all 2-HP-β-CD residues (1 to 14) and
report the results in file rms_CD.out
Georgios Leonis et al.