On Fri, May 30, 2014 at 2:12 PM, James Starlight <jmsstarlight.gmail.com>
wrote:
> Dear Amber Users!
>
>
> There are some questions about parametrization of the non-standart amino
> acids (using simplest antechamber method) and its further connection to the
> rest of the backbone.
>
> Should the initial pdb of the non standard residue be consisted of capped N
> and C termi with NH2 and COOH groups or alternatively with NH and CO? I've
> tried to parametrize the whole residue with both types of caps but
> eventually after its integration to the rest of the protein using
>
You should probably use the same strategy as the one used to parametrize
the charges of the other amino acids. You should probably also perform
charge equivalencing on the backbone charges to make sure it matches the
other amino acids (that have the same side-chain charge). It is probably
easier to use R.E.D. than antechamber for this particular task. (See
http://q4md-forcefieldtools.org/Tutorial/ for more information).
source leaprc.ff99SB
> source leaprc.gaff
> loadoff crq.lib
> loadamberparams crq.frcmod
> protein = loadpdb protein_with_crq.pdb
> bond protein.62.C protein.63.N1
> bond protein.63.C3 protein.66.N
>
>
> as the result the additional OXT and H atoms always have been wrongly added
> to the previous (62) and next (66) residues so the geometry of new two
> peptide bonds have been perturbed. How I could fix it?
>
You need to set a head and tail atom on your custom residue (_before_ you
use saveOFF to create crq.lib). Something like this:
set CRQ.1 tail CRQ.1.C3
set CRQ.1 head CRQ.1.N1
That way, tleap will know to connect it to adjacent residues via those two
atoms (and your "bond" commands will become unnecessary).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 30 2014 - 11:30:03 PDT
