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
Received on Fri May 30 2014 - 13:00:02 PDT
