Dear Carlos and David,
Thank you for your valuable
suggestions. But still I am unable to restrain the distance between my
desired atoms. One particular thing I noticed (after David asked me to use
LISTIN option in my input file) is that the O atom of water is not showing
in the pout file and it looks like
INITIAL restraints/deviations/energy contributions:
******
CB ( 1735)-O ( 2946) NSTEP1= 0
NSTEP2= 0
R1 = 0.000 R2 = 0.000 R3 = 0.000 R4 = 100.000 RK2 = 0.000 RK3 =
500.000
Rcurr: 1.857 Rcurr-(R2+R3)/2: 1.857 MIN(Rcurr-R2,Rcurr-R3):
1.857
You can see I have changed r3 value to 0 from 1.8 so that there is more
chances of me getting final value bellow 2 A.
As David asked I am knowing that the distance is not getting restrained by
calculating the distance from the pdb file generated by the final coordinate
file i.e. rst file.
Now the problem is that during equilibration i.e. MD I am unable to put
larger force constant i.e. rk3>50 is not getting permission showing shake
default. Now some of the results from the minimization is as bellow
Force constant (rk3) Final distance of the restrained
atoms
60 2.26
70 2.08
80 2.17
90 2.04
100 2.22
200 2.02
300 1.99
400 1.94
500 1.75
1000 1.83
5000 1.63
As you can see I am not getting the desired restrained (<2A) bellow force
constant 300. Another particular thing I observe that the restrained
distance if not linearly related to the force constant used.
The minimization and equilibration which I am using are as bellow
min.in
minimisation with solute restrain
&cntrl
imin=1,maxcyc=500,ncyc=250
ntpr=5,ntr=1, nmropt=1,
restraint_wt=1000.0
restraintmask=':1-164',
/
&wt type='END' /
LISTIN=pout
DISANG=rst.dist
eq.in
Heating up the system equilibration stage 1
&cntrl
nstlim=5000 dt=0.002, ntx=1, irest=0, ntpr=1, ntwr=1, ntwx=1,
tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
ntb=1, ntp=0,
ntc=2, ntf=2, nmropt=1,
nrespa=2,
&end
&wt type='END' /
LISTIN=pout
DISANG=rst.dist
And rst file is
#
# 111 VAL QQG 276 WAT O 1.8
&rst
ixpk= 0, nxpk= 0, iat=1735,2946, r1= .00, r2= .00, r3= 0.00, r4= 100.00,
rk2=0.0, rk3=500, ir6=1, ialtd=0,
&end
So what should I do? Please suggest.
On Fri, Apr 22, 2011 at 8:46 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Apr 22, 2011, nicholus bhattacharjee wrote:
>
> > Thank you for an quick reply. As mentioned earlier I
> > have used low force constant and very high value of r4. Still I am not
> able
> > to restrain the distance.
>
> Can you say (again?) what you evidence is that you are not restraining the
> distance? With this input:
>
> > # 111 VAL QQG 276 WAT O 1.8
> > &rst
> > ixpk= 0, nxpk= 0, iat=1735,2946, r1= .00, r2= .00, r3= 1.80, r4=
> > 100000.00,
> > rk2=0.0, rk3=10, ir6=1, ialtd=1,
> > &end
>
>
> there will be no lower bound, but the distance should never get much
> greater
> than 1.8 Ang. A 1 Ang. violation would lead to a penalty of 10 kcal/mol.
> What does your distance vs time output look like?
>
> It's often helpful to set LISTIN=POUT to double check on your input. There
> is no reason to set either ir6 or ialtd here, although I don't think they
> should hurt.
>
> As Carlos suggested, a short run with ntpr=1 is also very often helpful.
>
> > NMR restraints: Bond = 1452.510 Angle = 0.000 Torsion =
> 0.000
> > What dose this Bond value gives?
>
> This is the total energy of the distance restraints. "Bond" is a bad word
> here.
>
> ....dac
>
>
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>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Tue Apr 26 2011 - 06:30:02 PDT
