[AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu

From: Taylor, Miles <taylormi.oregonstate.edu>
Date: Wed, 23 Nov 2016 07:56:48 -0800

Dear Dave,

I was asked not to start a new topic, I am assuming that means keep the
email chain with this email: amber.ambermd.org. Let me know if I am

The exact command I have been using is: prepgen -i NRQ.ac -o NRQ.prepin -m
NRQ.mc -rn NRQ

If I am correct, the ./configure options used were: ./configure gnu

When I try to use "prepgen -i NRQ.ac -o NRQ.prepin" it also seems like it
works, but it isn't referencing my .mc file, which is designating the
backbone. Whenever I use -m NRQ.mc, I definitely get the error talked about

Thank you.


Please keep replies in the same thread rather than starting new topics (I
only say this because I've screwed up in the other direction, unwittingly
posting new threads in a previous topic).

When I run "prepgen -i NRQ.ac -o NRQ.prepin" I get NRQ.prepin with no seg
faults, although valgrind of that run reveals there is a memory error, an
invalid read, which definitely could cause a seg fault depending on your
compilation. Please post the ./configure options you used when building
Amber, and the exact command you used to run prepgen.


Miles Taylor
Graduate Student
Physical Chemistry
Department of Chemistry
Oregon State University
Corvallis, OR 97331
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Received on Wed Nov 23 2016 - 08:00:05 PST
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