Dear James,
> I'll try to spend time on RED tutorials before doing my parametrization.
I am glad I convinced you to use PyRED. uff ;-)
tutorial? it should take a few minutes:
- create a PDB file with hydrogen atoms with the two capping groups added:
Something like: MeCO-AA*-NHMe ; AA* being your new residue
- just define the two intra-mcc1 to be applied on your input molecule
in the Project.config file:
MOLECULE1-INTRA-MCC1 = 0.0 | a b c d e f | Remove
a - f are the indexes of the atoms of the capping group 1
for the first capping group...
MOLECULE1-INTRA-MCC1 = 0.0 | u v w x y z | Remove
u - z are the indexes of the atoms of the capping group 2
for the second capping group...
More generally see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
- if you do want to derive classical RESP charges for the
Amber99SB/Amber 10 force field no need to provide a System.config file.
- create the archive file:
tar zcvf archive.tgz Mol_red1.pdb Project.config
& upload it at
http://q4md-forcefieldtools.org/REDServer-Development/upload-log.php ;
you need to register only if you want to use Gaussian; no need to
register if you use Firefly or gamess...
> 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.
So you are not fully convinced ;-)
for blank topology of my residue? PyRED handles whole molecules and
molecular fragments; when you generate a molecular fragment you work
in same time on the whole molecule...
> 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?
Only PyRED generates the mol3 file format. You can obviously create
manually a mol3 file starting from a mol2 file; and Yes LEaP does
recognize that mol3 file format...
regards, Francois
> 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
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 31 2014 - 07:00:03 PDT
