AMBER Archive (2002)

Subject: Re: nmanal help request

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 27 2002 - 10:38:23 CDT

On Fri, Sep 27, 2002, Peter Fojan wrote:

> I try to do a quaish analysis of my md run in order to calculate the
> order parameters for my protein. The protein contains 1231 atoms. The
> quasih run finishes without problems but if I try to run nmanal, I
> always get teh following error message
> nmanal -O -i nmanal.in -o ubi.nmanal.out -p ubi.top -v ubi.quasih.vec -m
> mass -proj ubi.quasih.proj
>
> lib-4001 : UNRECOVERABLE library error
> A READ operation tried to read past the end-of-file.
>
> Encountered during a namelist READ from unit 4
> Fortran unit 4 is connected to a sequential formatted text file:
> "nmanal.in"
> IOT Trap
>
> nmanal.in
>
> &data

You probably need to put a space at the beginning of the above line: the "&"
character should be in column 2. Also, there has to be a title card before
the &data namelist (it's not clear from your e-mail whether you had this or
not...)

> ntrun = 7,
> nvect=80,
> ibeg=7, iend=80,

You don't want to set ibeg=7 for this sort of calculation: translation and
rotation have been removed by the superposition process before you ran quasih
(or should have been), so there will not be 6 rotation-translation modes to
skip. Follow the example on p. 257 and set ibeg=1.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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