Re: [AMBER] Using chirality restraints for modified residues

From: Bill Ross <>
Date: Fri, 29 Jun 2018 01:52:44 -0700

A chirality flip is likely facing an energy barrier, which maybe could
be easily graphed in someone's sophisticated workbench. :-)

I would fix it manually.


On 6/29/18 1:32 AM, Baptiste Legrand wrote:
> 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 > << EOF
> source leaprc.gaff
> source leaprc.ff99SB
> loadamberparams ./UNK.frcmod
> loadoff ./
> 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
> sander -O -i -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 - 02:00:03 PDT
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