Hello Jason,
Ok for the input file, I removed the redundant "/" or "&end" but that does
not produce any change.
I have tried to write the restraints in several way but always using the
"restraint = " keyword. I have unsuccessfully tried:
( :4.P :25.Na+ )
(:4.P,:25.Na+)
( (:4.P) (:25.Na+) )
(:4.P, 759)
(221 759)
and other combinations... never worked.
If I use the iat format instead, all seems to work but... I want to run 408
independent MD runs, in 408 different systems. In all the systems the
residues and atom names are the same but the index changes and I really dont
want to make 408 different RST files!
Thanking you in advance,
P.
2011/5/9 Jason Swails <jason.swails.gmail.com>
> On Mon, May 9, 2011 at 5:23 PM, Pablo Dans Puiggròs <pdans.mmb.pcb.ub.es
> >wrote:
>
> > Hi,
> > I'm trying to do some MD with sander.MPI and distance restraints
> (nmropt=1)
> > in AMBER 11.
> > No matter how I write the restraints I always get the same message:
> >
>
> How have you tried writing them? Try specifying atom numbers, and DON'T
> use
> the "restraint = " keyword. Use
>
> iat=10,15,
>
> Where 10 is replaced by the atom number of :4.P and 15 is replaced by the
> atom number of :25.Na+. One problem with this code is that it actually
> uses
> a completely separate mask parser, so you can't be sure that ambmask is
> parsing your masks in the same way that the restraint parser is.
>
> If this is the case, you may have uncovered a bug in that parser that we
> have to find/fix.
>
>
> > Error: Invalid atom or grouping specified in restraint.
> > restraint = "distance( :4.P :25.Na+ )"
> >
> > If I ask the ambmask about these atoms I get the right answer.
> >
> > This is my input file:
> >
> > ---------------------------------------------------
> > Equilibration
> > &cntrl
> > imin=0, irest=1, ntx=5,
> > ntt=1, tempi=298.15, temp0=298.15, tautp=2.5,
> > ntp=1, pres0=1.0, taup=2.5,
> > ntb=2, ntc=2, ntf=2, cut=10.0,
> > ntr=0, nmropt=1,
> > nstlim=250000, dt=0.002, t=0.0, nscm=5000,
> > ntpr=500, ntwx=500, ntwe=0, ntwr=5000,
> > &end
> > /
> >
>
> &end and / have the same function. Only include one of them (I don't know
> if that'll cause problems or not, but better safe than sorry)
>
>
> > &wt type='TEMP0',
> > istep1=0, istep2=0,
> > value1=298.15, value2=298.15,
> > /
> > &wt type='REST',
> > istep1=0, istep2=0,
> > value1=1.0, value2=1.0,
> > /
> > &wt type='END'
> > /
> > LISTIN=md2in.RST
> > LISTOUT=md2out.RST
> > DISANG=genericNaMG.RST
> > /
> > &end
> >
>
> The / and &end are not needed here at all (and may cause issues).
>
> Hope this helps,
> Jason
>
>
> > ---------------------------------------------------
> >
> > and this is my DISANG file:
> >
> > ---------------------------------------------------
> > &rst restraint = "distance( :4.P :25.Na+ )",
> > ifvari= 0,
> > ialtd= 0,
> > r1= 2.75,
> > r2= 2.75,
> > r3= 4.25,
> > r4= 4.25,
> > rk2= 5.0,
> > rk3= 5.0,
> > /
> > ---------------------------------------------------
> >
> > please guide me!
> >
> > thanks.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pablo Dans Puiggròs, PhD
Molecular Modelling & Bioinformatics Group
Institute for Research in Biomedicine
Barcelona Science Park
pablo.dans.irbbarcelona.org
pdans.mmb.pcb.ub.es
&
Biomolecular Simulations Group
Institute Pasteur of Montevideo
pdans.pasteur.edu.uy
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Received on Mon May 09 2011 - 10:00:03 PDT
