Dear all
We have started a protein-drug MD simulation, we found the following issues;
1) Few amino acids cleaved and detached from the main chain (469 amino acids ), after minimization of the complex.
2) After equilibration stage, the drug (C16H28N2O4) is considerably moved out ,compared to the X-ray crystallographic structure available in PDB.
We will be thankful to you if you recommend suggestions to troubleshoot the issues.
Inputs are mentioned below for your perusal
Minimization: Minimization to relax initial bad contacts, explicit solvent
&cntrl
imin=1,
ncyc=1000,
maxcyc=5000,
ntpr=50,
cut=8,
restraintmask='!:WAT&.CA,C,O,N'
restraint_wt=10.0,
/
Heat
Explicit solvent initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=1000, ntwx=1000, nstlim=200000,
dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, ntb=1,
iwrap=1, ioutfm=1, nmropt=1,
/
&wt
TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
Equilibration
Explicit solvent molecular dynamics constant pressure MD
&cntrl
imin=0, irest=1, ntx=5,
ntpr=1000, ntwx=1000, nstlim=2000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=1.0, ig=-1,
ntp=1, ntc=2, ntf=2, cut=8,
ntb=2, iwrap=1, ioutfm=1,
/
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Received on Tue Nov 24 2015 - 04:00:02 PST
