AMBER Archive (2008)

Subject: RE: AMBER: problem with group input and NMR restaints

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Nov 04 2008 - 10:16:34 CST

Hi,

I have tried with this input file also, but it is not reading the group file.
Is there any other way to do this.

Another option i tried is :
Stage 1
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=100000, dt=0.002,gbsa =1,surften=0.005,
  ntc=2, ntf=2,ntr=1,
  ntt=3, gamma_ln =5.0,
  tempi=0.000, temp0=300.19,
  ntpr=500, ntwx=500, ntwr = 500,
  ntb=0, igb=1,nmropt=1,
  cut=16,
  restraint_wt=1.0,
  restraintmask=':1-100'
  /
  &wt type= 'REST', istep1 =0, istep2=0, value1=1.0, value2=1.0, /
  &wt type='END' /
  DISANG=rst
  END

Will this restraint_wt=1.0,

  restraintmask=':1-100' do the same thing as the group do.

Regards
priya

--- On Tue, 4/11/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:
From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: AMBER: problem with group input and NMR restaints
To: amber_at_scripps.edu
Date: Tuesday, 4 November, 2008, 9:16 PM

Hi Priya,

I'm not sure if you can use NMR restraints with harmonic restraints, I have
never tried it although I don't see why it wouldn't work. With regards
to your input I think the group input has to come last. so your input should
probably be:

Stage 1
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=100000, dt=0.002,gbsa =1,surften=0.005,
  ntc=2, ntf=2,ntr=1,
  ntt=3, gamma_ln =5.0,
  tempi=0.000, temp0=300.19,
  ntpr=500, ntwx=500, ntwr = 500,
  ntb=0, igb=1,nmropt=1,
  cut=16
  /
 &wt type= 'REST', istep1 =0, istep2=0, value1=1.0, value2=1.0, /
 &wt type='END' /
  DISANG=rst
END
hold the protein fixed
10.0
ATOM 1 900
END
END

Although you may have to experiment here to be sure.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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