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 - 18:00:03 PST
