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://q4md-forcefieldtools.org/Tutorial/ 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
>>
>
>
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Received on Fri May 30 2014 - 12:30:03 PDT
