if you want to do a 2D umbrella sampling, you should first make sure you
understand the 1D version first. you'll need to scan combinations of the 2
retraints, and it can be more difficult to ensure overlap in 2D space than
with normal US (due to the diagonal overlap). You may end up wanting to
only scan a subset of the 2D space, but that depends a lot on your goals
and what you expect to happen.
As a side not, I always get very concerned about using distance and angle
for ligands - if you're sampling binding, there are many other degrees of
freedom besides these 2, and as the ligang gets close enough to contact the
receptor the barriers to sampling these motions can be very high (or even
impossible) once you have other things restrained. You'll need to really do
careful analysis of all of the motions other than the ones you sample with
US, and probably carry out fully independent runs starting from different
ligand locations and conformations. It's very easy to think it's converged
when in reality your restraints have just disconnected regions of phase
space that should all be sampled but no longer can be. just my opinion...
On Fri, Aug 12, 2016 at 6:49 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Thank you Carlos
>
> Yes I want to use both as umbrella restrain
>
> So how do I edit my script
>
>
> &wt type='DUMPFREQ', istep1=50 /
> &wt type='END' /
> DISANG=N_C_3.4
> DUMPAVE=dist_N_C_3.4.dat
> /
>
>
> Will adding one line behind angle restrain make it work?
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, August 12, 2016 11:22:27 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] umbrella sampling restraining both angle and distance
>
> You can restrain both, but it's not clear if you're asking if you can use
> both as umbrella restraints and change get the target values. If yes, the
> most direct way is to do 2D umbrella sampling, changing them independently.
>
> On Aug 12, 2016 12:50 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
>
> > Hi everyone,
> >
> > I was just wondering that is is possible to restrain both distance and
> > angle at a same time in umbrella sampling.
> >
> > What I want is to restrain my ligand at a distance between 1.2 to 3.4
> > angstrom and at an angle between 150 to 180 degrees.
> >
> >
> > Everywhere I can see either they restrain angle or distance.
> >
> >
> > Thanking you,
> >
> > Abhishek
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailman_listinfo_amber&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=vixAf5DPsc1rfcPyaBdH_520TbtVaVRdAUTuv8KI2eI&s=
> ahy7R6LH3yQmxnNe_fIYdy3oyfgwMS1Hilk2lX9vSAA&e=
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailman_listinfo_amber&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=vixAf5DPsc1rfcPyaBdH_520TbtVaVRdAUTuv8KI2eI&s=
> ahy7R6LH3yQmxnNe_fIYdy3oyfgwMS1Hilk2lX9vSAA&e=
> _______________________________________________
> 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 Sun Aug 14 2016 - 08:00:02 PDT
