AMBER Archive (2005)

Subject: Re: AMBER: atommask error

From: Sergio E. Wong (swon9_at_itsa.ucsf.edu)
Date: Fri Apr 29 2005 - 12:19:25 CDT


Thanks.. grouping the selection as you indicated worked. :)

On Fri, 29 Apr 2005 hornak_at_csb.sunysb.edu wrote:

> > Hi amber users;
> >
> > I am running into a problem using the restraint option ntr. My script
> > mdin file has the following lines:
> >
> > ntr = 1,
> > RESTRAINT_WT = 0.30,
> > restraintmask = ' :1-23_at_CA | :34-47_at_CA | :56-88_at_CA | :98-135_at_CA |
> > :146-160_at_CA | :168-206_at_CA | :213-999_at_CA ',
> >
> > I get the following error:
> >
> > Error in group input::atommask.f::pop_evalstack
> > stack underflow
>
> try grouping the residue spans into one term, such as:
> ':1-23,34-47,56-88_at_CA'
>
> the code is located in sander directory in atommask.f (unless this got
> renamed to somehting similar) and you should be able to locate the stack
> manipulation routines and the limits imposed on stack size...
>
> Cheers,
> -Viktor
>
> > if I reduce the number of terms in the restraint mask i.e.
> >
> > restraintmask = ' :1-23_at_CA | :34-47_at_CA | :56-88_at_CA | :213-999_at_CA ',
> >
> > Then there is no problem. I'm guessing there is some array length that
> > needs to be adjusted and the program recompiled. I just need to know
> > where in the source code is this parameter specified.
> >
> > Thanks
> >
> > -Sergio
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