I succeeded. The distance is maintained.
Thank you.
On Thu, Mar 7, 2019 at 8:07 PM Sundar <jubilantsundar.gmail.com> wrote:
> Did you succeed? Or do you still have questions?
>
> On Wed, Mar 6, 2019 at 10:02 PM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
>
> > Hi,
> > I already did this.
> > My restraint file used during minimization has following two lines.
> >
> > &rst iat=621,1399, r1=3, r2=5.0, r3=5.0, r4=7.0, rk2 = 20.0, rk3 = 20.0,
> /
> > &rst iat=1216,1400, r1=3, r2=5.0, r3=5.0, r4=7.0, rk2 = 20.0, rk3 =
> 20.0, /
> >
> > Here is my minimization parameter file:
> >
> > energy minimization
> > &cntrl
> > imin=1, maxcyc=2000, ncyc=1000,
> > ntwr=1000, ntpr=100, nmropt=1,
> > cut=999.0, rgbmax=999.0,
> > ntb=0, igb=5, saltcon=0.0,
> > /
> > &wt type='END', /
> > DISANG=dist_restaint.RST
> > DUMPAVE=dist_out.dat
> >
> > Thanks & regards,
> > Sunita
> >
> > On Wed, Mar 6, 2019 at 9:40 PM Sundar <jubilantsundar.gmail.com> wrote:
> >
> > > You can actually use ~/amber18/bin/makeDIST_RST script that comes with
> > > Amber to generate a restraint file and call it in min.in using
> nmropt=1
> > > with following to read in the generated distance restraint file.
> > >
> > > nmropt=1
> > > /
> > > &wt type='DUMPFREQ', istep1=10,
> > > /
> > > &wt type='END'
> > > /
> > > DISANG=../rst.dist ! To read in the restraint file
> > > DUMPAVE=dist_vs_t.txt ! To output the distance every simulation step
> > >
> > > Thanks,
> > > Jubilant
> > >
> > > On Sat, Mar 2, 2019 at 6:03 AM Sunita Patel <sunita.patel.cbs.ac.in>
> > > wrote:
> > >
> > > > Dear Users,
> > > >
> > > > I want to put distance restraint before minimization between two
> > atoms. I
> > > > was searching in the manual and archive and found following two ways.
> > > > Which one is more appropriate?
> > > > How to include them in "min.in" file? It's not clear to me.
> > > >
> > > > Thanks in advance for your help.
> > > >
> > > > With best regards,
> > > > Sunita
> > > >
> > > > ------------------------
> > > >
> > > > # Change distance between atoms 485 and 134 from 15 A to 20 A
> > > > &rst iat=485,134, r2=15., rk2 = 5000., r2a=20. /
> > > >
> > > > ---------------------------
> > > > &rst
> > > > ixpk= 0, nxpk= 0, iat= 10, 27, r1= 1.30, r2= 1.80, r3= 4.60, r4=
> > > 5.10,
> > > > rk2=0.0, rk3=32.0, ir6=1, ialtd=0,
> > > > &end
> > > > #
> > > > ---------------------------
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > Thanks,
> > > Sundar Thangapandian
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Thanks,
> Sundar Thangapandian
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>
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Received on Thu Mar 07 2019 - 20:30:02 PST
