Many thanks for information!
I'll try to spend time on RED tutorials before doing my parametrization.
However in cases when I need for blank topology of my residue (for
qm/calculations for instance) providing explicitly only its bonding to the
rest of the protein as I understood antechamber parametrization might be
enough.
Assuming that I'm providing residue with CO in tail and NH in head
positions (all atoms corresponds to the complex.pdb) could I provide mol3
file (with head and tail specification) to leap to build my complex?
James
2014-05-31 16:50 GMT+04:00 Parker de Waal <Parker.deWaal.vai.org>:
> 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
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >>
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> > >> >>
> Zb7ILPtGLqww&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinf
> > >> >> o%2famber
> > >> >>
> > >> >
> > >> >
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> > >
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> >
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> > ---
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Received on Sat May 31 2014 - 06:30:02 PDT
