Dear Amber Users,
I am equilibrating the solvent (in solvated protein-ligand complex) using the following parameters.
But at the end of heating phase itself (first 20 ps), after reimaging, I found that the solvent molecules forming
many hollow spaces on the surfaces. MD runs seem to be stable and fine (temp, energy, density, please see the
attached
.out file). Can anyone point out if anything wrong with these
parameters. Actually I noticed this trend only after running
equilibration
phase for another 20 ps and then minimizing ligand & binding site residues as next step. Then I went back
and produced pdb files for every step and recognized this problem. My next step would be to run
QM/MM minimization on these solvated complexes. Herewith I am attaching .out for MD heating phase.
**********
step 1
**********
complex: initial minimization - solvent and ions
&cntrl
imin = 1,
ntpr = 500,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
cut = 12.0
drms = 0.001
/
Hold the protein fixed
500.0
RES 1 285
END
END
************
step 2
***********
bztcomplex: initial minimization -entire system
&cntrl
imin = 1,
ntpr = 500,
maxcyc = 5000,
ncyc = 1000,
ntb = 1,
cut = 8.0
drms = 0.001
/
*********
step 3
***********
complex: heating phase MD - solvent and ions
&cntrl
imin = 0,
ntpr = 100,ntwx = 100, ntwr = 1000,
nstlim = 20000,dt = 0.001,
tempi = 0.0, temp0 = 300.0,
ntb = 1,
ntr = 1,
cut = 10.0
ntt = 3, gamma_ln = 1.0
/
Hold the protein fixed
10.0
RES 1 285
END
END
*********
step 4
*********
bztcomplex: equilibration phase MD - solvent and ions
&cntrl
imin = 0,irest=1, ntx=7,
ntb=2, pres0=1.0, ntp=1,
taup=2.0,
ntpr = 100,ntwx = 100, ntwr = 1000,
nstlim = 20000,dt = 0.001,
tempi =300.0, temp0 = 300.0,
ntr = 1,
cut = 10.0
ntt = 3, gamma_ln = 1.0
/
Hold the protein fixed
10.0
RES 1 285
END
END
**************************************************************
Thanks in advance for your valuable time and suggestions.
Senthil Natesan
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- application/octet-stream attachment: md1.out
Received on Fri May 14 2010 - 13:00:03 PDT
