leap can add the bond, but that doesn't automatically change the
peptide conformation to make the bond short. all leap will do is take
the conformation that you loaded or built, and create a bond. you will
need to minimize this or do some work in building your initial
conformation to get it right.
note that minimizing a long bond is VERY likely to cause other
problems, since the energy will eb high enough to invert chiralities,
flip amides and so on.
I suggest that if you don't have a good conformation to start with,
that you build it without the cyclic bond, and then create a distance
restraint in sander for these 2 atoms. then, use nmropt=1 to slowly
draw them together during MD, with a final distance the same or close
to the bond length. take the final structure, convert to pdb, and use
that as the initial structure for the prmtop that has the bond
defined.
On Fri, Jan 16, 2009 at 12:38 PM, Lake, Thomas
<thomas.lake08.imperial.ac.uk> wrote:
> Hello,
>
> I am trying to model a cyclic peptide, so I loaded the pdb into LEAP. I
> then created a bond between the two terminal residues, and then altered
> the partial charges and the atom types of these residues. In LEAP this
> seemed to work fine; I then created topology and coordinate files using
> saveamberparm. However when I loaded these into VMD, the bonds where
> the termini were linked are now massively distorted. In the LEAP editor
> there doesn't seem to be this problem. Can anyone help me.
>
> Thanks
>
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>
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Received on Sun Jan 18 2009 - 01:20:51 PST
