Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 4 Jun 2014 13:06:06 -0600

On Wed, Jun 4, 2014 at 9:38 AM, Geoffrey Gray <gmgray2.mail.usf.edu> wrote:
> Error: Ref Atom [C7 ] not found in NA base [THY ]
>
> This is due to the fact that C7 in the Amber force field is C5M in the
> charmm force field.

Yikes - this is an unfortunate result of my lack of experience with
charmm. Right now the atom names for the NA bases are hard-coded at
the top of the file
$AMBERHOME/AmberTools/src/cpptraj/src/AxisType.cpp. I eventually need
to make it so you can load up a custom reference, but for now the
workaround is to change the atom name for that base in AxisType.cpp
and recompile. However, I would do this in a separate directory so
that you don't accidentally lose anything. I'm attaching a version of
AxisType.cpp where I have made this modification so you can see what I
mean.

Thanks for the report!

-Dan

>
> How can I fix this? I tried playing around with resmap, but this was
> unsuccessful.
>
> My script is
>
> ###
> parm dcd/dna.psf
> trajin dcd/merged-dna.dcd dcd
>
> nastruct naout na.dat resrange :3-33
> ###
>
>
> Thanks
>
> Geoffrey
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)



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Received on Wed Jun 04 2014 - 12:30:02 PDT
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