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://q4md-forcefieldtools.org/REDServer-Development/
- 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://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
- R.E.D. Server Dev. proposes a way to automatically generate
molecular fragments for nucleotide and amino acid residues;
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26
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://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#15
- Now if I look at your ligand:
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=NRQ&sid=3SVO
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://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26 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://q4md-forcefieldtools.org/REDServer-Development/faq.php#5
"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://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
>> >>
>> >
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> http://scanmail.trustwave.com/?c=129&d=n9aI04O_7nnrRUFxQw-xOsSH7lxbYpZb7ILPtGLqww&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2famber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 31 2014 - 01:30:03 PDT
