Dear Amber users,
I want to run constant pH MD simulations for one protein, which contains a
ligand, in explicit water with Amber14. First, I minimized the system with
a constraint on the protein backbone atoms, and there was nothing wrong in
the minimization. Then I wanted to heat the system from 0 K to 300 K. But
the system always collapsed, and the heating procedure died. I guess it is
the ligand's problem, because when I heated the system without the ligand,
it could safely heat to 300 K. I calculated the atomic charges of the
ligand in AM1-BCC charge model with antechamber, and I think there was
nothing wrong in this process. And I have checked the initial structure of
ligand, it looked reasonable. Can anyone tell me why ? The following is the
heating input file:
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=12, ntb=1,
iwrap=1, ioutfm=1, nmropt=1,
/
&wt
TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
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Received on Sun Oct 19 2014 - 12:00:02 PDT
