AMBER Archive (2004)

Subject: Re: AMBER: sander.QMMM on Mac

From: justin litchfield (litch_at_stanford.edu)
Date: Sat Nov 27 2004 - 02:29:26 CST

Ross,
and by the way, the tutorial simulations worked fine, just not on my
system. perhaps i should try neutralizing my system? when i add Cl-
ions though it seems to distort the molecule into a weird conformation
in the minimization.

justin

On Nov 26, 2004, at 5:56 PM, Ross Walker wrote:

> Dear Justin,
>
>> Ò¡RROR IN OPNFIL -- CANNOT OPEN UNIT 8 FILE _è¦|||#x8_at_H
>> ERROR IN OPNFIL -- CANNOT OPEN UNIT 77 FILE ¦¿ÿð!ÿ 
>
> Please try the following and let me know how you get on.
>
> 1) Apply bugfix.13 and bugfix.26 to your amber src tree.
>
> 2) Replace $AMBERHOME/src/divcon/divcon.h with the attached divcon.h
>
> 3) Completly recompile amber 8. (Make sure you do a make clean in
> $AMBERHOME/src before making.)
>
> 4) Ensure you have a divcon.in file in the directory in which you are
> running your simulation - see $AMBERHOME/test/qmmm/standard for an
> example. Or
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six/
> index.htm.
>
> 5) Re-run your simulation and then contact me to let me know how it
> worked. If you have problems please send me all your input and output
> files and as much info (error messages etc) as you can.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 |
> | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> <bugfix.13><bugfix.26><divcon.h>
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