Date: Mon, 7 Nov 2011 17:18:13 +0000
Dear AMBER users,
I was trying to equilibrate the protein system as well as the cubic water box surrounded but something unexpected happened.
When equilibration (after minimization) started the structure suddenly went into a mess (refer to the image attached to this mail).
BTW, when I shifted "ntb=1" into "ntb=0" in the heating step, the structure was well. I'm wondering that is there anything wrong with the periodic boundary condition? Plus, I've checked structures generated by minimization steps and they are all right.
Below are scripts which I utilized to generate the solvent box, add sodium ions, saving parameter and topology files and did minimization works.
-----------------------------------------------------------------------
> tleap
> source leaprc.gaff
> source leaprc.ff99SB
> source leaprc.ff10
> comp = loadpdb structure.pdb
> solvatebox comp TIP3PBOX 8.0
> addions comp Na+ 0
> saveoff comp structure.off
> loadamberparams frcmod.ionsjc_spce
> saveamberparm comp structure_wb.prmtop structure_wb.inpcrd
-----------------------------------------------------------------------
Initial minimization ------water
&cntrl
imin=1,
maxcyc=5000,
ncyc=2500,
ntwx=100,
ntb=1,
ntr=1,
cut=10.0,
restraint_wt=5.0,
restraintmask=':1-396'
/
-----------------------------------------------------------------------
Initial minimization ------all
&cntrl
imin=1,
maxcyc=2500,
ncyc=1250,
ntwx=100,
ntb=1,
ntr=0,
cut=10.0
/
-----------------------------------------------------------------------
Heating - solvent and ions
&cntrl
imin=0,irest=0,ntx=1,
ntb=1,cut=10.0,
ntr=1,
restraint_wt=0.5,
restraintmask=':1-396',
ntc=2,ntf=2,
tempi=0.0,temp0=300.0,ntt=3,gamma_ln=1.0,
nstlim=20000,dt=0.001,
ntpr=100,ntwx=100,ntwr=200
/
-----------------------------------------------------------------------
I'm quite appreciate if anybody could give me a hand.
Many thanks,
X. Li
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(image/png attachment: md_result.png)
