Jason,
I've already done it but it could not help (the wrong atoms have been added
to the adjacent residues in any case).
source leaprc.ff99SB
source leaprc.gaff
crq = loadmol2 crq_amber.mol2
loadamberparams crq.frcmod
set crq tail crq.1.C3
set crq head crq.1.N1
saveoff crq crq.lib
Should I define special types for NH and CO groups of my non standard
residue?
James
2014-05-30 22:25 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> 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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>
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Received on Fri May 30 2014 - 12:30:03 PDT
