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 Thu Nov 10 2022 - 18:30:03 PST
