AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules]

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Dec 21 2008 - 21:08:38 CST

Taufik,

I tested your system again, but now I solvated it with water. I followed
the same minimization procotol. After 5000 steps, I see the NMR restraints
still working (went down from 12 kcal/mol to 0.32 kcal/mol in this
period). Looks like that nmropt=1 works fine.

On Sat, 20 Dec 2008, Taufik Al-Sarraj wrote:

> That is what i noticed also, I am relieved. thank you Ilyas.
> My simulation did not work when i used ntb=1 and solvated the system
> with water.
> but when i used ntb=0 and eedmeth = 5. The restraint in the simulation
> worked
> same as the tutorial
> http://www.uni-koeln.de/themen/Chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm
>
> Thank you again for all your help,
> Taufik
>
> Ilyas Yildirim wrote:
> > Taufik,
> >
> > I tried a couple tests on your structure, and whether I use a group of
> > atoms or single atom to define at1 or at2, everything works fine. Did you
> > try to re-install amber and see if that will solve the problem? If not, I
> > will send you all the tests I've done. I am using amber9 by the way.
> >
> > On Fri, 19 Dec 2008, Taufik Al-Sarraj wrote:
> >
> >
> >> Potentially dangerous attachments were identified and removed from this
> >> message.
> >>
> >> of course,
> >>
> >> RSTdel is the original RST file and RST4 is the one i modified manually
> >> to have the correct atom number.
> >>
> >> Best,
> >> Taufik
> >>
> >>
> >
> >
>
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-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
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