Hi Karl,
Sorry but not sure I can help. I always did my prep files in interns, since
then the torsion structure is clear a d it's easier to see how things like
chirality work. I don't know a good way to understand connections from the
cartesians...
Carlos
On Jul 11, 2013 10:53 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
wrote:
> Hi Carlos (and those who are curious),
>
> Perhaps you can see something that is wrong with the prep file that I
> can't. Below are the prep files, one for each enantiomer. These were
> designed using the guide in http://ambermd.org/doc/prep.html and through
> comparison to the tree structures in the amino acid prep files. The
> difference is that these prep files contain Cartesian rather than internal
> coordinates.
>
> Bests,
> Karl
>
> ----
> leap.in:
>
> logfile leap.log
> source leaprc.ff99SB
>
> loadAmberPrep PML.prep
> loadAmberPrep PMD.prep
>
> poly = sequence {PMD PML}
>
> 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.1.C4 poly.1.C5 poly.1.C3 poly.1.C2
> measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
>
> ----
> PML.prep:
>
> 0 0 0
>
> l stereoisomer of PMMA
> PML.res
> PML INT 0
> CHANGE NOMIT DU BEG
> 0.00000
> 1 DUMM DU M 0.000000 0.000000 0.000000 0.0
> 2 DUMM DU M 1.000000 0.000000 0.000000 0.0
> 3 DUMM DU M 1.000000 1.000000 0.000000 0.0
> 4 C3 CT M 7.225283 1.596329 -0.000010 0.0122
> 5 C5 CT 3 7.463912 0.743730 1.260042 0.0051
> 6 H6 HC E 7.277746 1.318591 2.162413 0.0000
> 7 H7 HC E 6.825308 -0.130844 1.274038 0.0000
> 8 H8 HC E 8.497868 0.412590 1.286041 0.0000
> 9 C2 C B 5.780539 2.084531 -0.000006 0.7775
> 10 O2 O E 5.441307 3.225154 -0.000006 -0.6079
> 11 O1 OS S 4.910133 1.081546 -0.000004 -0.4792
> 12 C1 CT 3 3.536914 1.422858 -0.000002 0.2872
> 13 H1 H1 E 2.999797 0.487044 -0.000002 0.0000
> 14 H2 H1 E 3.287731 1.998614 -0.880328 0.0000
> 15 H3 H1 E 3.287809 1.997454 0.881103 0.0000
> 16 C4 CT M 8.162226 2.808418 -0.000014 0.0051
> 17 H4 HC E 9.194555 2.474469 -0.000018 0.0000
> 18 H5 HC E 8.004066 3.428113 0.873973 0.0000
>
> IMPROPER
> C3 O2 C2 O1
> C2 C5 C3 C4
>
> DONE
> STOP
>
> ----
> PMD.prep:
>
> 0 0 0
>
> d stereoisomer of PMMA
> PMD.res
> PMD INT 0
> CHANGE NOMIT DU BEG
> 0.00000
> 1 DUMM DU M 0.000000 0.000000 0.000000 0.0
> 2 DUMM DU M 1.000000 0.000000 0.000000 0.0
> 3 DUMM DU M 1.000000 1.000000 0.000000 0.0
> 4 C3 CT M 7.225283 1.596329 -0.000010 0.0122
> 5 C5 CT 3 7.463871 0.743848 -1.258927 0.0051
> 6 H6 HC E 8.497801 0.412707 -1.285950 0.0000
> 7 H7 HC E 6.825276 -0.130715 -1.273935 0.0000
> 8 H8 HC E 7.277769 1.317569 -2.162036 0.0000
> 9 C2 C B 5.780539 2.084531 -0.000006 0.7775
> 10 O2 O E 5.441307 3.225154 -0.000006 -0.6079
> 11 O1 OS S 4.910133 1.081546 -0.000004 -0.4792
> 12 C1 CT 3 3.536914 1.422858 -0.000002 0.2872
> 13 H1 H1 E 2.999797 0.487044 -0.000002 0.0000
> 14 H2 H1 E 3.287731 1.998614 -0.880328 0.0000
> 15 H3 H1 E 3.287809 1.997454 0.881103 0.0000
> 16 C4 CT M 8.162226 2.808418 -0.000014 0.0051
> 17 H4 HC E 9.194555 2.474469 -0.000018 0.0000
> 18 H5 HC E 8.003078 3.428025 -0.873884 0.0000
>
> IMPROPER
> C2 C5 C3 C4
> C3 O2 C2 O1
>
> DONE
> STOP
>
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Tuesday, July 9, 2013 6:42:02 PM
> Subject: Re: [AMBER] Residue chirality
>
> 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 Thu Jul 11 2013 - 09:30:02 PDT
