AMBER Archive (2002)

Subject: Re: Protein jump out, please help

From: Lich Nguyen (nguyenthanhlich_at_yahoo.com)
Date: Thu Oct 24 2002 - 22:21:40 CDT

Dear Amber experts,

I would like to say thank Dr Arvid Soederhaell, Dr
Michael G Cooney and Dr Michael Crowley for your help.

I guess my protein moving into the neighbouring
periodic image of the box. I am not sure but I don’t
know how to check. If it just moves to neighbouring
image, is this acceptable? I thought something must be
wrong so my protein is moving away? Can I just try
using ptraj to center the coordinates after MD and it
will be fine?
Does this phenomenon happen often?

Sorry, I haven’t got much knowledge in this field.
What do you mean by constant current through the
box???

Best wishes,

Lich Nguyen

Bioinformatic Lab
Institute of Biotechnology
NCST, Hanoi, Vietnam

--- Arvid Soederhaell <arvid_at_fmp-berlin.de> wrote:
> Hi Lich
>
> Are you sure that the protein actually leaves the
> box? Is it not just
> moving into the neighbouring periodic image of the
> box? (That does not
> really change the results of the simulation, unless
> there is a constant
> current through the box...)
>
>
>
> Arvid Soederhaell
>
>
> On Thu, 24 Oct 2002, Lich Nguyen wrote:
>
> >
> > Dear Amber experts,
> >
> > I am new Amber user. I am entering this forum
> seeking
> > your advice.
> > My problem is my protein jumping out of the water
> box,
> > which is a truncated waterbox216. I use Amber7 and
> > force field 99.
> > After minimization, my protein is well surrounded
> by
> > water. I continued to heat up my system to 305K.
> This
> > is my input file:
> >
> > &cntrl
> > imin=0, nmropt=1
> > nstlim=10000, dt=0.001,
> > ntpr=50, ntwr=1000, iwrap=1, ntwx=200,
> > ntf=2, ntc=2, ntb=1,
> > ntt=1,
> > &end
> > &wt type='TEMP0',
> istep1=0,istep2=1000,value1=0.0,
> > value2=5.0, &end
> > &wt type='TEMP0',
> istep1=1001,istep2=5000,value1=5.0,
> > value2=100.0, &end
> > &wt type='TEMP0',
> > istep1=5001,istep2=10000,value1=100.0,
> > value2=305.0, &end
> > &wt type='TAUTP',
> istep1=0,istep2=5000,value1=0.5,
> > value2=0.5, &end
> > &wt type='TAUTP',
> > istep1=5001,istep2=10000,value1=0.5,
> > value2=0.1, &end
> > &wt type='END' &end
> >
> > I haven’t known how to use Moil-view so I make a
> pdb
> > file from trajectory output file. My protein
> already
> > jumped out after the first time frame (after
> 200fs).
> > About 1/4 of my protein is outside waterbox.
> >
> > Second, I tried to change some features. This is
> my
> > new input file:
> >
> > &cntrl
> > imin=0, nmropt=1
> > nstlim=50000, dt=0.001,
> > ntpr=50, ntwr=1000, iwrap=1, ntwx=200,
> > ntf=2, ntc=2, ntb=1,
> > ntt=1, nscm=10, tautp=0.1
> > &end
> > &wt type='TEMP0',
> istep1=0,istep2=10000,value1=0.0,
> > value2=5.0, &end
> > &wt type='TEMP0',
> > istep1=10001,istep2=25000,value1=5.0,
> > value2=100.0, &end
> > &wt type='TEMP0',
> > istep1=25001,istep2=50000,value1=100.0,
> > value2=305.0, &end
> > &wt type='END' &end
> >
> > My protein still jump out.
> >
> > Third, I tried to heat up my protein using
> temperature
> > ramp with the temp at the beginning already 305K
> and
> > everything restrain. Next, I would losen some
> restrain
> > atoms.
> >
> > # Equilibration of solvent and hydrogens
> > &cntrl
> > imin=0, nstlim=2500, dt=0.002,
> > ntx=1, irest=0, ntr=1,
> > ntpr=50, ntwx=200, ntwr=2500, iwrap=1,
> > ntf=2, ntc=2, tol=0.00000001, ntb=2,
> > tempi=305.0, temp0=305.0,
> > ntt=1, tautp=0.5,
> > pres0=1.0, ntp=1, taup=0.6,
> > &end
> > Group input for amino acid restrains
> > 50.0
> > FIND
> > * * M *
> > * * B *
> > * * S *
> > * * 3 *
> > SEARCH
> > RES 1 468
> > END
> > Group input for ion/substrate restrains
> > 50.0
> > RES 469
> > END
> > END
> >
> > Just after this running, I see my protein is
> already
> > out of the water box.
> >
> > What is happening? Why iwrap=1, small NSCM or
> restrain
> > almost every atom doesn’t help? My protein always
> goes
> > out and the water box deformed.
> >
> > I greatly appreciate any advice. Please help
> >
> > Best wishes,
> > Lich Nguyen
> >
> >
> >
> > __________________________________________________
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> >
>

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