[AMBER] Generating parameters for unnatural amino acids

From: Suchetana Gupta via AMBER <amber.ambermd.org>
Date: Thu, 10 Nov 2022 17:44:18 -0800

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
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