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
Received on Wed Mar 06 2019 - 20:30:02 PST
