The sign ":" is for specifying RESIDUES not ATOMS..
since you have a dipeptide i.e composed of 2 residues, you can't specify
":7-20,26-38" as there is no residue numbered beyond 2..
you need to specify atoms using "." instead of ":"..
So you should specify like ".7-20,26-38"
Cheers
On 3/22/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> try restraintmask='7-20,26-38'
> for more information, please read the manual, there is
> an example of just this kind of selection. p287 for amber9.
>
>
> On 3/22/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> > hi amber users
> >
> > I am using restraint command in sander during minimization of a
> > dipeptide (phenylalanine- dehydrophenylalanine). I a using the
> > following command which is giving thew following error
> >
> >
> >
> > [root.Bic11 exe]# sander -O -i min.in -o delphe_rest.min.out -c
> > delphe_rest.x -p prmtop -r delphe_rest.min.x
> >
> > At line 1022 of file _mdread.f (Unit 5 "min.in")
> > Traceback: not available, compile with -ftrace=frame or -ftrace=full
> > Fortran runtime error: In line 1 of namelist cntrl:
> > Bad name
> > restraintmask=':7-20', '
> >
> > ^
> >
> > I have to restrain the movement of atoms 7-20 and 26-38
> >
> >
> > i am giving the following input file
> >
> >
> > min.in
> >
> > energy minimization for delphe starting structure
> >
> > &cntrl
> > imin=1, maxcyc=10, ncyc=5, ntpr=1,
> > ntb=0,cut=15.0, ntr=1, restraint_wt=1.0,
> > restraintmask=':7-20', ':26-38',
> > &end
> > &ewald
> > eedmeth=5,
> > &end
> >
> >
> > i cant understand where i am going wrong
> >
> > please guide me
> >
> > thanks
> > deepti
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> \
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
sandy_thesmitten
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 28 2007 - 06:07:20 PDT
