AMBER Archive (2009)

Subject: RE: [AMBER] generalized distance restraint

From: Rausch, Felix (frausch_at_ipb-halle.de)
Date: Wed Mar 11 2009 - 02:39:05 CDT

Thanks for your suggestions.

While reading up on how ABMD works, I went through the Tutorial B10, too. I
found out that the Addin for Amber10 described there (LCOD) is exactly what i
was looking for. So i (hopefully) just have to follow instruction given
there.

Regards,
Felix Rausch

-----Ursprüngliche Nachricht-----
Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im
Auftrag von M. L. Dodson
Gesendet: Montag, 9. März 2009 17:51
An: AMBER Mailing List
Betreff: Re: [AMBER] generalized distance restraint

On Mon, Mar 09, 2009 at 12:39:43PM -0400, Carlos Simmerling wrote:
> well I can't say much about the jar option, but in your case you
> didn't write an end to the first restraint so sander probably thinks
> there is only 1. maybe someone else can say whether jar with >1
> restraint will work.
>

I think with the regular SMD setup using NMR-type restraints, only the
first restraint is "steered" when jar is turned on. Any other
restraints are treated as regular NMR-style restraints, so must
satisfy the syntax rules for those. There may be a way to do multiple
steered restraints, but if so I don't know how.

I think you can do what you want using SMD within the ABMD-formalism.
I have gone over to that type of SMD setup exclusively. You can mix
regular NMR-style restraints with an AMBD-style SMD setup (or any of
the other ABMD-derived designs, probably).

Bud Dodson

>
>
> On Mon, Mar 9, 2009 at 12:15 PM, Rausch, Felix <frausch_at_ipb-halle.de>
wrote:
> > Thank you for your fast reply.
> > Im sorry that my first mail wasnt accurate enough.
> >
> > Until now, i started all my Steered MDs with Amber10 for free energy
> > calculations with restraints like this:
> >
> > &rst iat=8879, 8458, r2=2.625, rk2=50, r2a=1.0,
> > /
> >
> > With the jar option set to 1 for SMD, the missing parameters will be set
> > automatically. In the output, the restraint looks like the following:
> >
> > jar option running
> > ******
> >  H82 ( 8879)-OH  ( 8458)                            NSTEP1=     0
> > NSTEP2=500000
> > R1 = -97.375 R2 =   2.625 R3 =   2.625 R4 = 102.625 RK2 =  50.000 RK3 =
> > 50.000
> > R1A= -99.000 R2A=   1.000 R3A=   1.000 R4A= 101.000 RK2A=  50.000 RK3A=
> > 50.000
> >  Rcurr:    2.626  Rcurr-(R2+R3)/2:    0.001  MIN(Rcurr-R2,Rcurr-R3):  
 0.001
> >                       Number of restraints read =     1
> >
> > Now i want to start a SMD with two different restraints running in
parallel
> > over the time of a MD (described in the manual p. 168f ?). Goal is the
same
> > as  doing a normal SMD, a free energy calculation. So i thought just
adding
> > another &rst line to the REST-file would work, but i only get an error
> > message or only the first restraint is recognized.
> >
> > Input .REST:
> >
> > &rst iat=4676, 1583 r2=3.792, rk2=50, r2a=1.00,
> > &rst iat=4657, 4671 r2=3.897, rk2=50, r2a=1.5,
> > /
> >
> > Output:
> >
> >  jar option running
> > ******
> >  H5  ( 4676)-OD1 ( 1583)                            NSTEP1=     0
> > NSTEP2=250000
> > R1 = -96.208 R2 =   3.792 R3 =   3.792 R4 = 103.792 RK2 =  50.000 RK3 =
> > 50.000
> > R1A= -99.000 R2A=   1.000 R3A=   1.000 R4A= 101.000 RK2A=  50.000 RK3A=
> > 50.000
> >  Rcurr:    3.792  Rcurr-(R2+R3)/2:    0.000  MIN(Rcurr-R2,Rcurr-R3):  
 0.000
> >                       Number of restraints read =     1
> >
> >                    Done reading weight changes/NMR restraints
> >
> >
> >
> > I hope that someone tried a similar task or has an example of such
> > restraint(s) so i can get an idea of how to fit my values to the required
> > format given in the manual.
> >
> > Thanks,
> > Felix Rausch
> >
> >
> >
> > -----Original Message-----
> > From:   amber-bounces_at_ambermd.org on behalf of Carlos Simmerling
> > Sent:   Mon 3/9/2009 4:13 PM
> > To:     AMBER Mailing List
> > Cc:
> > Subject:        Re: [AMBER] generalized distance restraint
> > does the restraint you sent actually work? I would think maybe no, due
> > to missing commas and not defining some of the variables like r3 etc.
> > maybe the defaults are ok, but read the sander output carefully to
> > make sure it is exactly what you want.
> > regarding multiple restraints, it is certainly possible to set
> > multiple restraints and have them all changing at the same time.
> > whether you need "generalized" restraints depends on what you are
> > trying to do, which you haven't really said. is this for a free energy
> > calculation? do you need a single restraint that changes multiple
> > distances? try to clarify and more people might be able to help out.
> >
> >
> >
> > On Mon, Mar 9, 2009 at 9:48 AM, Rausch, Felix <frausch_at_ipb-halle.de>
wrote:
> >>
> >> Dear amber users,
> >>
> >> I already started some Steered MD caclulations. Since I cant get the
> >> makeDIST_RST program work properly I generated the REST-files by hand.
They
> >> look like the following:
> >>
> >>  &rst iat=4676, 1583 r2=3.792, rk2=50, r2a=1.00,
> >>  /
> >>
> >> Now i want to set up a calculation with 2 constraints at the same time,
> >> something like "Decrease distance between atoms A and B while increasing
> >> distance between atoms C and D". I read in the manual that this is
possible
> >> by the use of a generalized distance restraint constraint.
> >>
> >> Is there anybody who already set up such a job who can maybe help me
> >> generating a REST-file for this task? Despite reading the manual, im not
> > sure
> >> how to modify my REST-file to set the right parameters.
> >>
> >> Thanks in advance,
> >> Felix Rausch
> >>
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> >>
> >
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-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

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