Suchetana,
the tutorial you are referring to describes the parameterization of an
isolated, i.e. not covalently bound, organic ligand. This is a small
entity described completely with gaff.
When parameterizing an unnatural amino acid, the situation is different,
since your resulting entity has to have open valences (C-terminus /
N-terminus), i.e. the leap mechanism has to understand and choose the
correct connectivity, and you have to decide, which parameters to be
used that they fit to the rest of the system, and maybe validate your
resulting parameter set.
Since parameterization is an advanced task in MD simulations, you have
to ensure that really know what you're doing there. (And the workflow
might not be that straightforward in all cases.)
Thus, I'd suggest not only to read the manual and work through the
tutorials, but also have a look into the literature, where people
described parameterization procedures similar to those you are in need of.
Maybe that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 11.11.2022 um 03:03 schrieb Suchetana Gupta via AMBER:
> To follow up on this:
> The Leap output structure looks fine. However the connectivity seems to be
> lost in the minimization step.
>
> The minimization file used is:
> min (no shake, belly minimization of hydrogens in waters)
> &cntrl
> imin = 1, maxcyc = 500, ncyc = 250, ntr = 1, ntb =0, igb = 0, cut=20.0
> &end
> Restrain all heavy atoms
> 30.0
>
> SEARCH
> RES 1 8
>
> END
> END
>
>
> Please help me with where I am going wrong!
>
> Thanks
> Suchetana
>
> On Thu, Nov 10, 2022 at 5:44 PM Suchetana Gupta <suchetana.gupta.gmail.com>
> wrote:
>
>> Hello
>> I am trying to generate parameters for some unnatural amino acids
>> following the instructions here at
>> https://ambermd.org/tutorials/basic/tutorial4b/index.html
>>
>> The commands used are:
>>
>> antechamber -i abc.pdb -fi pdb -o abc.mol2 -fo mol2 -c bcc -s 2
>>
>> parmchk2 -i abc.mol2 -f mol2 -o abc.frcmod
>>
>>
>> leap_abc.in:
>>
>> source leaprc.protein.ff14SB
>>
>> source leaprc.gaff
>>
>> ABC = loadmol2 abc.mol2
>>
>> check ABC
>>
>> loadamberparams abc.frcmod
>>
>> saveoff ABC abc.lib
>>
>> saveamberparm ABC abc.prmtop abc.inpcrd
>>
>> quit
>>
>>
>> antechamber -i xyz.pdb -fi pdb -oxyz.mol2 -fo mol2 -c bcc -s 2
>>
>> parmchk2 -i xyz.mol2 -f mol2 -o xyz.frcmod
>>
>> leap_xyz.in:
>>
>> source leaprc.protein.ff14SB
>>
>> source leaprc.gaff
>>
>> XYZ = loadmol2 xyz.mol2
>>
>> check XYZ
>>
>> loadamberparams xyz.frcmod
>>
>> saveoff XYZ abc.lib
>>
>> saveamberparm XYZ xyz.prmtop xyz.inpcrd
>>
>> quit
>>
>> My peptide has two unnaturals and I am using the following Leap input file:
>>
>> source leaprc.protein.ff14SB
>> source leaprc.gaff
>> loadamberparams xyz.frcmod
>> loadamberparams abc.frcmod
>> loadoff xyz.lib
>> loadoff abc.lib
>> seq = { A B C D E F G }
>> cycpep = loadPDBusingseq peptide.pdb seq
>> bond cycpep.1.N cycpep.8.C
>> savepdb cycpep peptide_out.pdb
>> saveAmberParm cycpep peptide.top peptide.crd
>> quit
>>
>>
>>
>> However, the leap output PDB and hence subsequent structures from
>> minimization etc show no connection/bonds between the unnatural amino acids
>> residues and the other residues.
>>
>> Where am I going wrong?
>> I have used this similar approach for other general cyclic peptides and
>> hence I am guessing I may have made a mistake in the parameter generation.
>>
>> Can someone please help me here?
>>
>> Thanks!
>>
>> Suchetana
>>
>>
>>
>>
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Received on Fri Nov 11 2022 - 02:30:02 PST
