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----
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,
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jul 11 2013 - 09:00:04 PDT