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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 07 2019 - 07:00:04 PST
