I'll try running the pdb file through pdb4amber.
I've been looking at tutorials B4 and B5 because I'll eventually have to do
force field calculations, but first I have to get the proper pdb for my
molecule.
Thank you so much for your help!
On Wed, Jul 26, 2017 at 5:32 AM, David Case <david.case.rutgers.edu> wrote:
> On Fri, Jul 21, 2017, Akshar Sharma wrote:
>
> > I did try that, but it seems that in order to use addresidue() , I would
> > have to define a residue library for my special residues in the directory
> > $AMBERHOME/dat/reslib which I'm not sure how to do...
> > Is there any way to use addresidue without doing this?
> > Otherwise, how do I define a residue library (is there any book or
> website
> > that could teach me how to?)
>
>
> If you just need the coordinates (say in PDB format, for some other
> application), things should be much simpler. If the residue numbers
> are not correct, try running the pdb file you get through pdb4amber. You
> will
> have to make sure that your input pdb file has TER cards after each strand
> (aka
> chain).
>
> If you need to carry out force field calculations, you'll have to learn how
> to make libraries for modified residues. See, e.g. tutorials B4 and B5.
> But
> you might not need NAB for that...
>
> ....dac
>
>
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Received on Tue Jul 25 2017 - 21:30:02 PDT
