Hi James,
Yes, to use R.E.D. servers you need to provide a fully protonated ligand/non-standard residue.
Good luck,
Parker
________________________________________
From: James Starlight [jmsstarlight.gmail.com]
Sent: Saturday, May 31, 2014 7:50 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Parametrization of non-standart residues
Dear Francois,
many thanks for suggestions! I'll try to test PyRED for the chromophore
(I've correctly recognized N1 atom is heap and C3 is tail). One question:
should I provide residue with all hydrogens to R.E.D?
James
2014-05-31 10:11 GMT+02:00 FyD <fyd.q4md-forcefieldtools.org>:
> Dear James,
>
> In a former email you said "I've already done it but it could not help
> (the wrong atoms have been added to the adjacent residues in any case)."
> -> I did not find any record about a job with your email address at
> R.E.D. Server Dev.
>
> I continue to think you should use R.E.D. Server Dev./PyRED at
> http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1Q1x3nZdA&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fREDServer-Development%2f
>
> - I want to underline that PyRED can generate force field library to
> the mol3 file format, which contains information about head/tail for a
> molecular fragment; so no need to define them manually or to convert a
> mol2 into a off file. See
> http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyTwFlnn-Fcw&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fTutorial%2fleap-mol3%2ephp
>
> - R.E.D. Server Dev. proposes a way to automatically generate
> molecular fragments for nucleotide and amino acid residues;
> See http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1Vgmy_UJg&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fTutorial%2fTutorial-4%2ephp%2326
> these approaches are for classical atom connectivities between
> 'classical' molecular fragments...
>
> For more complex cases a user can still use the intra-mcc1/2 and
> inter-mcc1/2 keywords; which allow the generation of potentially any
> type of molecular fragments...
> See http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1Y8znCFeQ&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fTutorial%2fTutorial-4%2ephp%2315
>
> - Now if I look at your ligand:
> http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1U0nSvRIw&u=http%3a%2f%2fwww%2ercsb%2eorg%2fpdb%2fligand%2fligandsummary%2edo%3fhetId%3dNRQ%26sid%3d3SVO
> this is not clear to me how you can generate a head and a tail for
> this molecule; it looks like you have an imine function at N1 and a
> carboxylic acid at C3; and I guess that two positions are where you
> want to connect that residue in your protein...
>
> Obviously here the automatic procedure reported at
> http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1Vgmy_UJg&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fTutorial%2fTutorial-4%2ephp%2326 cannot
> work; but using two intra-mcc1 for the COMe (pseudo_imine-COMe if I
> well understood...) and NHMe capping groups should do the job. For
> that residue I would not use gaff, but FF atom types as defined in
> parm99... PyRED generates a LEaP script that can be modified to extend
> its applications.
>
> Once the first job executed at R.E.D. Server Dev.
> see http://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyTwYznCrZJA&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fREDServer-Development%2ffaq%2ephp%235
> "When describing the problem you encountered with R.E.D. Server
> Development, please also provide the 'PXXXX' R.E.D. Server Development
> job name in the body of your email so that we can more easily assist
> you."
>
> For sure here PyRED will generate unknown FF parameters for your
> residue, but they can be generally solved; you can provide a
> frcmod.user input file in that case in a second Re_Fit job.
>
> I hope this helps...
>
> regards, Francois
>
>
> > 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://scanmail.trustwave.com/?c=129&d=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyT1U0nSvRIw&u=http%3a%2f%2fwww%2ercsb%2eorg%2fpdb%2fligand%2fligandsummary%2edo%3fhetId%3dNRQ%26sid%3d3SVO
> 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=psKJ03PnxgRUfF-7TV12OHwM4dV7TqVyTwFhzHyFcQ&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
> >> >> _______________________________________________
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> >> >> o%2famber
> >> >>
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> >> >
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>
>
> F.-Y. Dupradeau
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Received on Sat May 31 2014 - 06:00:02 PDT
