How did you set up the tree in the prep file? My guess is something there
is inconsistent or not what leap can handle.
On Jul 9, 2013 11:29 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
wrote:
> Hi Carlos and Jason,
>
> I ran into this problem when I was working on a model for creating a
> short strand of PMMA polymer several years ago. (Granted, not something
> that Amber was originally created to handle.) Since these residues were
> nonstandard, I built my own prep files and linked them together in xleap
> using the sequence command, as one would do for a peptide.
>
> When I measure the prep file's improper torsion angle around the chiral
> center using the measureGeom command, for one residue (PMD) I obtain a
> value of +119.5, and for the other (PML) I obtain -119.5.
>
> When I do the same measurement, but now one the short "polymer"
> (BEG-PML-PMD-END), I obtain values of -118.5 (PML) and -118.5 (PMD).
>
> Unless I am missing something, this shows that PMD had its chirality
> altered by xleap. Granted, that I may have introduced an error into the
> prep files, but I have triple checked them. Also note that if I were to
> save the BEG-PML-PMD-END as a pdb file, and opened it up in an external
> viewer, there are incorrect bonds added to the molecule due to
> inappropriate short distances-- so I know that the prep files are not
> conformationally optimized for the sequence command. Not really knowing the
> leap code, I still didn't expect the change in chirality.
>
> All of this was done using: "Latest patch applied to AmberTools12: 31".
> The leap input and part of the log file are included below. If you see
> something obvious in my thoughts or the leap input, I would appreciate
> hearing it. (I personally do not need this example to be solved, and I use
> it only for demonstrating what I encountered before.)
>
> Bests,
> Karl
>
> leap input:
> -----------
> logfile leap.log
> source leaprc.ff99SB
>
> loadAmberPrep BEG.prep
> loadAmberPrep PML.prep
> loadAmberPrep PMD.prep
> loadAmberPrep END.prep
>
> poly = sequence {BEG PML PMD END}
>
> measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
> measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2
>
> measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
> measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2
>
> leap.log:
> ---------
> > measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
> Torsion angle: -119.48 degrees
> > measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2
> Torsion angle: 119.50 degrees
>
> > measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
> Torsion angle: -118.47 degrees
> > measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2
> Torsion angle: -118.47 degrees
>
>
>
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Tuesday, July 9, 2013 2:06:05 PM
> Subject: Re: [AMBER] Residue chirality
>
> I've done this in tleap many times and it does work. The issue here is
> probably in the details. What was the old a new sidechain? What is nearby?
> When leap built it, did it fit without clash? Was the chivalry wrong coming
> from leap, or after some minimization?
>
> Note that leap can do this, but it won't try to optimize the location. In
> most cases you probably want to use a different program to build initial
> structures, not leap. Swisspdb does a reasonable job of sidechain
> placement.
> On Jul 9, 2013 5:25 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
> wrote:
>
> > Hi,
> >
> > At one time there was a bug concerning this in tleap (and g/sleap??),
> > and I am not sure if it was ever corrected. If I recall correctly, the
> only
> > work-around I found was to construct the enantiomer using an external
> > editor (e.g. PyMol) and load it into xleap. This preserved the
> connectivity
> > and dihedral angles.
> >
> > Cheers,
> > Karl
> >
> > ----- Original Message -----
> > From: tdo.chem.ucsb.edu
> > To: amber.ambermd.org
> > Sent: Tuesday, July 9, 2013 11:07:58 AM
> > Subject: [AMBER] Residue chirality
> >
> > Hello,
> >
> > I try to perform mutations on a peptide by removing the sidechain atoms
> > and replacing the old residue names with new residue names, then letting
> > tleap add in the missing atoms. I check the chirality of the residues and
> > find out that I don't have the correct chirality (i.e., I compute the
> > chirality dihedral angles and obtain both positive and negative numbers).
> >
> > Is there any better way to do mutations with Amber/tleap? How can I fix
> > the incorrect chirality?
> >
> > Thank you,
> >
> >
> >
> >
> >
> >
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Received on Tue Jul 09 2013 - 10:00:02 PDT
