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.rosswalker.co.uk> wrote:
From: Ross Walker <ross.rosswalker.co.uk>
Subject: RE: AMBER: problem with group input and NMR restaints
To: amber.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
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Fri Dec 05 2008 - 10:42:19 PST
