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.
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?
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?
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
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> > 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 - 03:00:04 PDT
