[AMBER] Heating Problem

From: jinfeng liu <jinfengliu1119.gmail.com>
Date: Sun, 19 Oct 2014 11:49:21 -0700

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
   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,
   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
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