thank you carlos and sandeep. i have corrected the error and now i am
able to run the minimization.
On 3/26/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> good catch, I didn't notice the dipeptide part, I just looked for the cause
> of
> the error message (the comma syntax)
>
> On 3/26/07, Sandeep Kaushik <sandy.thesmitten.gmail.com> wrote:
> > 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
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Received on Wed Mar 28 2007 - 06:07:34 PDT
