Dear All,I have analyzed intermolecular hydrogen bonding of two different simulation trajectories via amber16 cpptraj, but got different resultsSimulation1 production run input file===========================
NPT production with no restrains
&cntrl
imin=0, ntx=7, irest=1, ntrx=1, ntxo=1,
ntpr=500, ntwx=500, ntwv=500, ntwe=500,
ntf=2, ntb=2, cut=8.0,
nsnb=100, igb=0,
nstlim=500000,
t=0.0, dt=0.002,
ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
vlimit=20,
ntp=1, taup=1.0, pres0=1.0, comp=44.6,
ntc=2, tol=0.00000001,
/
hbond.in========trajin 4hld_prod1.mdcrd.gz
trajin 4hld_prod2.mdcrd.gz
trajin 4hld_prod3.mdcrd.gz
trajin 4hld_prod4.mdcrd.gz
trajin 4hld_prod5.mdcrd.gz
autoimage
strip :WAT
strip :Na+
hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat
as a result of above pasted script, I just got ligand and residues interactions.
Run======
CPPTRAJ: Trajectory Analysis. V16.12
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 01/16/17 14:41:01
| Available memory: 150.184 MB
Reading '../4hld.prmtop' as Amber Topology
INPUT: Reading input from 'h_bond.ptraj'
[trajin ../4hld_prod1.mdcrd.gz]
Reading '../4hld_prod1.mdcrd.gz' as Amber Trajectory
[trajin ../4hld_prod2.mdcrd.gz]
Reading '../4hld_prod2.mdcrd.gz' as Amber Trajectory
[trajin ../4hld_prod3.mdcrd.gz]
Reading '../4hld_prod3.mdcrd.gz' as Amber Trajectory
[trajin ../4hld_prod4.mdcrd.gz]
Reading '../4hld_prod4.mdcrd.gz' as Amber Trajectory
[trajin ../4hld_prod5.mdcrd.gz]
Reading '../4hld_prod5.mdcrd.gz' as Amber Trajectory
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
[strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
[strip :Na+]
STRIP: Stripping atoms in mask [:Na+]
[hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat]
HBOND: Searching for Hbond donors/acceptors in region specified by *
Only looking for intermolecular hydrogen bonds.
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing # Hbond v time results to 4hld_hbond.agr
Writing Hbond avgs to 4hld_av_hbond.dat
---------- RUN BEGIN -------------------------------------------------
Simulation2 production input file==========================
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 1000, ntwx = 500, ntwr = 1000
/
hbond.in========trajin md_simulation1.mdcrd.gz
trajin md_simulation2.mdcrd.gz
trajin md_simulation3.mdcrd.gz
trajin md_simulation4.mdcrd.gz
trajin md_simulation5.mdcrd.gz
trajin md_simulation6.mdcrd.gz
trajin md_simulation7.mdcrd.gz
trajin md_simulation8.mdcrd.gz
trajin md_simulation9.mdcrd.gz
trajin md_simulation10.mdcrd.gz
autoimage
strip :WAT
strip :Na+
hbond All nointramol out nhb.agr avgout avghb.dat
Run========
CPPTRAJ: Trajectory Analysis. V16.12
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 01/16/17 14:41:16
| Available memory: 8227.6 MB
Reading 'GHEA-quercetagetin_01.prmtop' as Amber Topology
INPUT: Reading Input from file h_bond.ptraj
[trajin md_simulation1.mdcrd.gz]
Reading 'md_simulation1.mdcrd.gz' as Amber Trajectory
[trajin md_simulation2.mdcrd.gz]
Reading 'md_simulation2.mdcrd.gz' as Amber Trajectory
[trajin md_simulation3.mdcrd.gz]
Reading 'md_simulation3.mdcrd.gz' as Amber Trajectory
[trajin md_simulation4.mdcrd.gz]
Reading 'md_simulation4.mdcrd.gz' as Amber Trajectory
[trajin md_simulation5.mdcrd.gz]
Reading 'md_simulation5.mdcrd.gz' as Amber Trajectory
[trajin md_simulation6.mdcrd.gz]
Reading 'md_simulation6.mdcrd.gz' as Amber Trajectory
[trajin md_simulation7.mdcrd.gz]
Reading 'md_simulation7.mdcrd.gz' as Amber Trajectory
[trajin md_simulation8.mdcrd.gz]
Reading 'md_simulation8.mdcrd.gz' as Amber Trajectory
[trajin md_simulation9.mdcrd.gz]
Reading 'md_simulation9.mdcrd.gz' as Amber Trajectory
[trajin md_simulation10.mdcrd.gz]
Reading 'md_simulation10.mdcrd.gz' as Amber Trajectory
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
[strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
[strip :Na+]
STRIP: Stripping atoms in mask [:Na+]
[hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat]
HBOND: Searching for Hbond donors/acceptors in region specified by *
Only looking for intermolecular hydrogen bonds.
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing # Hbond v time results to 4hld_hbond.agr
Writing Hbond avgs to 4hld_av_hbond.dat
While for second one, I got both residue-residue and residue-ligand interaction. Why results of both simulation hydrogen bond analysis is different even I have used same system and script for running these analysis. The first one results just ligand and residue interaction while other one is printing both residue-residue and residue ligand hydrogen bond.
Where am I going wrong? Thanks in advance for any suggestions.
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Received on Mon Jan 16 2017 - 03:00:02 PST
