Hello,
If I run makeCHIR_RST, I get output constraining certain angles/dihedrals in my protein (including my LES region of interest). If I want to do simulated annealing LES using restraints, then I need to change the restraints output from makeCHIR_RST to account for new LES atom numbers. (like that done with makeDIST_RST or makeANG_RST). Right? Could do this "by hand" or attempt some script writing of my own, but either would take quite awhile...
As an aside, a separate LES issue I am having currently (I know I am doing something dumb, just can't put my finger on it currently).
Getting the following error when attempting to run sander.LES:
ERROR: Flag "BOND_FORCE_CONSTANT" not found in PARM file
Amber tests run fine. Using my parm with amber tests - does not work fine (repeat error). Not sure what I have or haven't done to my parm to get this error. Examined test parm vs. my parm - couldn't discern a difference in the BOND_FORCE_CONSTANT section.....
Thanks!
Jamie
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Friday, February 19, 2010 9:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] makeCHIR_RST and LES
can you be more specific about what you want to do? it could be very quick
depending on how you are using LES.
On Wed, Feb 17, 2010 at 11:34 AM, Titus, Jamie (bairdje) <
BAIRDJE.ucmail.uc.edu> wrote:
> Hello all,
>
> Any chance of a quick code modification for getting LES appropriate output
> from makeCHIR_RST (assuming of course that I have correctly deduced that
> such an option does not currently exist)?
>
> Thanks!
>
>
> Jamie
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>
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Received on Fri Feb 19 2010 - 08:00:03 PST
