Hi Parker,
I've tried it too. Result was the same
Added missing heavy atom: .R<CPHE 62>.A<OXT 21>
Added missing heavy atom: .R<crq 63>.A<OXT 39>
Created a new atom named: H within residue: .R<NSER 64>
Can I upload mol2 of residue to some service so you could check my initial
coordinates? I suppose that the error might be here :) OR alternatively
see this link
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=NRQ&sid=3SVO I've
made parametrization of this residue in the sasme capped neitral form
2014-05-30 23:43 GMT+04:00 Parker de Waal <Parker.deWaal.vai.org>:
> Hi James,
>
> In the second tleap you shouldn't need to bond your non-standard residue
> to the backbone (assuming there isn't a ter card between them). By setting
> the head and tail atoms for the crq residue leap will recognize and
> automatically bond them to the corresponding head and tail atoms in protein
> sequence.
>
> Best,
> Parker
>
> -----Original Message-----
> From: James Starlight [mailto:jmsstarlight.gmail.com]
> Sent: Friday, May 30, 2014 3:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Parametrization of non-standart residues
>
> Also please find below full workflow which I've used during
> parametrization of new residue
>
>
> 1 -- parametrization
>
> antechamber -i crq_dr.mol2 -fi mol2 -o crq_amber.mol2 -fo mol2 -c bcc -s 2
> -at amber
>
> parmchk -i crq_amber.mol2 -f mol2 -o crq.frcmod
>
>
> 2 -- using tleap for residue
>
> source leaprc.ff99SB
> source leaprc.gaff
> crq = loadmol2 crq_amber.mol2
> loadamberparams crq.frcmod
> set crq head crq.1.N1
> set crq tail crq.1.C3
> saveoff crq crq.lib
>
> 3-- using tleap for complex (protein + new residue)
>
> source leaprc.ff99SB
> source leaprc.gaff
> loadoff crq.lib
> loadamberparams crq.frcmod
> GmKate = loadpdb GmKate_ph7.pdb
> bond GmKate.62.C GmKate.63.N1
> bond GmKate.63.C3 GmKate.66.N
> check GmKate
> savepdb GmKate xz.pdb
> #saveoff GmKate GmKate.lib
>
> #saveamberparm GmKate GmKate.prmtop GmKate.inpcrd
>
>
> James
>
>
> 2014-05-30 23:00 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
>
> > 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://scanmail.trustwave.com/?c=129&d=n9aI04O_7nnrRUFxQw-xOsSH7lxbYpZb7NKasG_oww&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fTutorial%2f
> 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://scanmail.trustwave.com/?c=129&d=n9aI04O_7nnrRUFxQw-xOsSH7lxbYp
> >> Zb7ILPtGLqww&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinf
> >> o%2famber
> >>
> >
> >
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Received on Fri May 30 2014 - 23:30:02 PDT
