AMBER Archive (2007)

Subject: Re: AMBER: restraint in minimization

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Mar 26 2007 - 06:19:13 CST

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_at_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_at_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_at_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_at_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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu