Adding restraint_wt=30.0, restraintmask=‘:1’, worked a treat. Thanks very
much to both of you for the explanation and suggestion!
On Tue, Sep 23, 2014 at 9:27 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> On Sep 23, 2014, at 3:20 PM, George Green <soyo.green.gmail.com> wrote:
>
> > I tried the modification you suggested, but still no joy. Still getting
> the
> > same error. It seems to indicate that there is something wrong with the
> > distance restraint file. However, I checked and atom numbers, etc seem
> all
> > correct. What do you think?
>
> It is definitely not the distance restraint file. The “rfree” subroutine
> that is throwing the error here handles the free-format parsing of the card
> section following the namelists in the input file. It has nothing to do
> with the NMR restraints. And as you’ve seen, the parser is not forgiving.
>
> I seem to recall that the order of the cards at the bottom of the input
> file matters. It could be that pmemd is trying to interpret the DISANG and
> LISTOUT lines as GROUP input. You could try moving those to the end of the
> input file.
>
> However, unless you _need_ to use the GROUP input for the positional
> restraint definitions [1], I would suggest using restraint_wt and
> restraintmask instead. That way, you avoid the whole problem.
>
> For example, add:
>
> restraint_wt=30.0, restraintmask=‘:1’,
>
> to the &cntrl namelist variables. [2] Then you can get rid of the
> restraint section at the bottom of the input file.
>
> HTH,
> Jason
>
> [1] For positional restraints, the only thing I know you can do with the
> GROUP input that you cannot do with restraintmask and restraint_wt is
> restrain different selections with restraints of different strengths.
>
> [2] The restraint of 30 kcal/mol/A^2 is very strong. I believe that this
> is actually _twice_ the strength of the restraint force constant (since I
> don’t think it’s multiplied by 1/2 like in Hooke’s law). I typically use 1
> kcal/mol/AA for ‘weak’ restraints and 5-10 for ‘strong’ restraints.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 23 2014 - 14:30:02 PDT
