AMBER Archive (2002)

Subject: Re: Protein jump out, please help

From: Michael G Cooney (chemgc_at_panther.Gsu.EDU)
Date: Thu Oct 24 2002 - 13:51:52 CDT

Dear Dr. Nguyen,

This might be a translational problem, since you seem to be using periodic
boundary conditions, which can cause the solute to jump to another unit
cell where the water is not visible (the crd gives only one water box).
You might try using ptraj (a program to process the trajectory, hence the
name) to center the coordinates after MD; the AMBER web site gives more
information on this. Good luck; I hope this is the problem and that ptraj
solves it.

Sincerely,

Michael G. Cooney
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303, USA

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,
v> 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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