Re: [AMBER] Using chirality restraints for modified residues

From: Baptiste Legrand <>
Date: Fri, 29 Jun 2018 11:43:44 +0200

I should modify manually the PDB file, save it as mol2 and then use the
loadmol2 command to then save my prmtop and inpcrd/rst file? Thanks Bill.


Le 29/06/2018 à 10:52, Bill Ross a écrit :
> 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.
> Bill
> 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
>> EOF
>> 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 - 03:00:03 PDT
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