Thanks Carlos and David for your answers,
I'm trying to prepare a cyclic peptide using non natural amino acids.
The cyclization typically occurs via the side chains of these amino
acids (UNK). So, I prepared the building block using antechamber and I
used tleap via the following script to prepare the molecules. The linear
peptide is good, the two UNK residues have the right chiralities. The
problem occurs when I cyclized the peptide using leap, after the
minimization step. The chirality of the CA of the first UNK was
inverted. Thus, the idea was to constrained the chirality of UNK in a
subsequent short MD step after the minimization. Unfortunately, for the
moment it failed. May be, such constraints prevent the chirality flips
but cannot "re-invert" bad chiralities?
cat > leap.in << EOF
source leaprc.gaff
source leaprc.ff99SB
loadamberparams ./UNK.frcmod
loadoff ./UNK.off
PEP = sequence { ACE GLU LEU ARG PRO ARG ASP UNK TYR LEU ILE UNK ARG PRO
NHE }
remove PEP PEP.8.H13
remove PEP PEP.8.H14
remove PEP PEP.8.C8
remove PEP PEP.12.H13
remove PEP PEP.12.H14
remove PEP PEP.12.C8
remove PEP PEP.12.H3
bond PEP.8.C7 PEP.12.C7
saveamberparm PEP ./JMV6294_cyc.prmtop ./JMV6294_cyc.inpcrd
quit
EOF
sander -O -i min.in -o ./JMV6294_cyc.out -c ./JMV6294_cyc.inpcrd -p
./JMV6294_cyc.prmtop -r ./JMV6294_cyc.rst
ambpdb -aatm -p ./JMV6294_cyc.prmtop < ./JMV6294_cyc.rst > ./JMV6294_cyc.pdb
Thanks.
Best,
Baptiste
Le 28/06/2018 à 20:31, David A Case a écrit :
> On Thu, Jun 28, 2018, Baptiste Legrand wrote:
>> When I launched calculations on pseudopeptides incorporating non-natural
>> residues, I had chirality issues. So I would try to fix it using the
>> chirality restraints on my non-standard residues. I first modified the
>> makeCHIR_RST file to incorporate these latter and to simply use the
>> makeCHIR_RST command but it still ignore them.
> There must be some reason for this. The usual debugging strategy is to
> set LISTIN=POUT in your input file: this will give detailed information
> about how each restraint is being processed at the first step. You can
> make sure that what you prepared is being read and interpreted in the
> way you intended.
>
> The makeCHIR_RST script just simplifies the creation of restraints, but
> they look exactly like ones that could be hand-generated. You could
> copy and paste them insided your .dist file if you want. There is not
> enough information in your email to tell why the chirality restraints
> are being ignored, but there has to be rational reason.
>
> ....dac
>
>
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Received on Fri Jun 29 2018 - 02:00:02 PDT
