Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously

From: Jason Swails <>
Date: Tue, 23 Sep 2014 16:27:20 -0400

On Sep 23, 2014, at 3:20 PM, George Green <> 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.


[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
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 23 2014 - 13:30:03 PDT
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