Re: [AMBER] Using chirality restraints for modified residues

From: Bill Ross <>
Date: Fri, 29 Jun 2018 03:21:41 -0700

Manually modify in xleap, or another graphic program if you have a
preference. xleap allows relaxing selected atoms according to general
hybridization geometries, but it's not the most used or polished
interface for that purpose I believe.

You don't need to have a new mol2 file, since the connectivity is the
same. Either loadpdb your fixed pdb from another program, or fix it in
xleap and saveamberparm from there (maybe savepdb at that point too, to
have the new coords in easy reference form).


On 6/29/18 2:43 AM, Baptiste Legrand wrote:
> 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.
> Baptiste
> 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 - 03:30:02 PDT
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