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.
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 09 2011 - 09:00:03 PDT
