Hello,
On Thu, Aug 12, 2010 at 5:57 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Jason,
>
>
>
> Thanks for your comments. As I cannot find the place to define w1,w2 in
> manual, so, I did not know how to input this.
>
It is not called w1, w2, ..., in the input file. They are the values for
rstwt.
>
>
>
> Is it correct to say:
>
>
>
> # reaction coordinates
> &rst iat=1,2,2,3, r1=0., r2=1., r3=1., r4=10., w1=1, w2=-1, rk2 = 30., rk3
> = 30., /
>
>
> If atom A,B,C has atom numbers of 1, 2 and 3, respectively?
>
No. It should be this:
#reaction coordinates
&rst iat=1,2,2,3, r1=0., r2=1., r3=1., r4=10., rstwt=1,-1, rk2=30, rk3=30, /
>
>
>
> The reasons why I use iat(6) previously is because I found the manual said
> iat=6 is used to define reaction coordinate. If it not necessary to have
> iat(6) in the restraint file, do I still not to define it is iat=6 so as to
> differentiate reaction coordinates restainst from distance/angle/torsion
> restraint? Did I misunderstood the manual?
>
I believe you did. When the manual mentions iat(#) where # is some number,
they mean that "number" of the iat array. For example, iat(6) references
the 6th number of the iat array, which in your case doesn't exist. The
manual says when iat(5)=0, it's either a torsion restraint if rstwt(1)=0
(the first element of rstwt, which in the example above is 1) or a
generalized distance restraint of 2 distances. When iat(7)=0, it's a
generalized distance of 3 distances, or when iat(8) is NOT 0, it's a
generalized distance of 4 distances (if rstwt(4) is also not zero) or a
plane-plane angle restraint. To more fully explain the input file above,
iat(1)=1, iat(2)=2, iat(3)=2, iat(4)=3 and rstwt(1)=1, rstwt(2)=-1.
Hope this helps,
Jason
>
>
> Best regards with many thanks,
>
>
>
> Cat
>
>
>
>
>
> > Date: Wed, 11 Aug 2010 08:46:42 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] How to define "generalized distance coordinate
> restraint" in AMBER10?
> >
> > On Wed, Aug 11, 2010 at 5:55 AM, Catein Catherine <
> askamber23.hotmail.com>wrote:
> >
> > >
> > > Dear All,
> > >
> > >
> > >
> > > I would like to calculate a PMF for a reaction coordinates which
> involve
> > > forming bond between A-B, at the same time cleaving a bond between B-C.
> > >
> > >
> > >
> > > I learnt from Bud that I may use "generalized distance coordinate
> > > restraint" to set the restraint and define the reaction coordinates. I
> > > lookup the manual. I found the restaint is defined as
> > >
> > >
> > >
> > > U = k(w1|r1-r2|+w2|r3-r4|+w3|r5-r6|+w4|r7-r8|-r0)2
> > >
> > >
> > >
> > >
> > >
> > > Is it same as the restrainst defined for LCOD?
> > >
> > >
> > >
> > > I also want to reconfirm with you that if I should define the restraint
> > > files as follows, if I want to study the PMF when LCOD change from 1A
> to
> > > 10A?
> > >
> > >
> > > # reaction coordinates
> > > &rst iat(6)=A,B,B,C, r1=0., r2=1., r3=1., r4=10., rk2 = 30., rk3 = 30.,
> /
> > >
> >
> > This should be iat, not iat(6). You also need numbers here, not letters,
> > but I assume you knew that. If you want a generalized distance restraint,
> > you also need to define the restraint weights (rstwt). Then that will be
> a
> > generalized distance restraint for the 2 distances. The restraint weights
> > are the w1, w2, ..., etc. in the formula you posted above.
> >
> > Good luck!
> > Jason
> >
> >
> > >
> > > Best regards,
> > >
> > > Catherine
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 12 2010 - 05:00:03 PDT
