Awesome, thanks, Dan!
Geoffrey
On Wed, Jun 4, 2014 at 3:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
>
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Received on Wed Jun 04 2014 - 12:30:03 PDT
