hi Jason,
I mean I don't want xleap to automatically change A(rna) to A5, etc. Also
I'm switching from leaprc.ff03.r1 to leaprc.ff10. It seems it's using a
different pdb format. For example, in ff03, RNAs are RA, RG, etc. Instead in
ff10, they are R, G, etc. I modified the pdb file. However I couldn't get
the ions right. This is what I have in the pdb file:
HETATM 2826 Mg Mg+ 2574 108.723 40.309 -33.966 1.00 96.56
MG
No matter how I changed the name of the ion. It just can't get through
xleap. Thanks again.
Victor
On Thu, Sep 29, 2011 at 4:06 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Sep 29, 2011 at 4:54 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
>
> > hi all
> >
> > I''m using a truncated structure and I prefer the program not to label
> the
> > terminus. How can I do that? Thanks.
> >
>
> What do you mean "label"? What program are you using? We need a more
> detailed question to be able to help.
>
> If you mean that you don't want charged termini added automatically, then
> cap your structure with one of the neutral caps (ACE, NME, NHE, etc).
>
> HTH,
> Jason
>
>
> >
> >
> > Victor
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 29 2011 - 14:30:05 PDT
