What did you use to view? If you have used amber cordinates option then u
have to use amber coordinates with periodic box option to view
On Mon, Nov 7, 2011 at 10:48 PM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
> 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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>
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Mon Nov 07 2011 - 09:30:07 PST
