Re: nmanal help request

From: David A. Case <>
Date: Fri 27 Sep 2002 08:38:23 -0700

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 -o ubi.nmanal.out -p -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:
> ""
> IOT Trap
> &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

> 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

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Fri Sep 27 2002 - 08:38:23 PDT
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