of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: https://hutchisonlab.org/
On Jan 15, 2024 at 2:41:00 PM, David van der Spoel
wrote:
Dear devs,
my group have worked on implementing a better representation of the GAFF
atomtypes, as well as our own set of atomtypes
https://github.com/dspoel/openbabel
Is there any interest to include any of this into the main openbabel
repository? I would then port my changes to the latest openbabel and
submit a pull-request.
Cheers,
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala
1
Sodium is converted to Nitrogen and Chloride to Carbon. I tried meddling
with the atomtyp.txt file but to no avail. Any suggestions to make this
work as it should?
Thanks,
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchem
nBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så i
e.net/lists/listinfo/openbabel-discuss
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David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att
On 2021-05-01 13:02, David van der Spoel wrote:
Hi,
I have the issue in the subject when running obenergy on a Gaussian log
file, using
obenergy -ff GAFF 123-trimethyl-imidazolium.log > log.out
When I instead use a sdf file there is no problem.
obenergy -ff GAFF 123-trimethyl-imidazolium.
3naAR
> 4ccAR
> 5naAR
12,13c12,13
< 8h1NO
< 9h1NO
---
> 8h4NO
> 9h4NO
Suggestions for debugging welcome.
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchem
not show my hydrogen, so I do not trust it.
On Sun, 25 Apr 2021, 13:28 David van der Spoel,
mailto:david.vandersp...@icm.uu.se>> wrote:
On 2021-04-25 14:09, Peter Jarowski wrote:
> Hi David:
>
> I would suggest you avoid inchi entirely for this as it has its
at 12:52, David van der Spoel
mailto:david.vandersp...@icm.uu.se>> wrote:
Hi,
I would like to generate an Inchi fro my compound but without adding
hydrogens. Is there a flag for that?
Here is an example for an acid and its deprotonated form that
yields the
same
(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40)
% obabel -oinchi -isdf perfluorotridecanoate.sdf
InChI=1S/C13HF25O2/c14-2(15,1(39)40)3(16,17)4(18,19)5(20,21)6(22,23)7(24,25)8(26,27)9(28,29)10(30,31)11(32,33)12(34,35)13(36,37)38/h(H,39,40)
--
David van
the -D_GLIBCXX_DEBUG from the CMAKE_CXX_FLAGS_DEBUG line in
CMakeLists.txt resolves the issue.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.u
ng,
which is rudimentary and duplicated between codes, should be fixed
first. I would think that OB should use the same command line flags for
the same variable in different codes.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala Universi
Den 2018-03-07 kl. 08:17, skrev David van der Spoel:
Den 2018-03-07 kl. 04:15, skrev spamidig:
Geoffrey, David:
Here is what I have for the openbabel on the g09 output file. Please
let me
know if you can not get the file as uploaded.
Thanks,
Sudhakar.
../openbabel-2.3.2/build/bin/obabel -i
g list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www
iscuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www
sites, Slashdot.org! http://sdm.link/slashdot
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Head
ive torsion). I will use the autodock tools
for now, have no time to investigate this further.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.ic
://pubchem.ncbi.nlm.nih.gov/compound/20022
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
#!/usr/bin/env python3
from pybel import *
import os, argparse
l 454-gaff.pdb
>
> The attached screenshot is what I get.
>
>
>
> On Mon, Jan 9, 2017 at 4:30 PM, David van der Spoel
> <sp...@xray.bmc.uu.se> wrote:
>> On 09/01/17 16:08, Eiso AB wrote:
>>> (installation: Open Babel 2.4.0)
>>>
>>> I'm gett
ng list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596,
t bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
> reports.http://sdm.link/zohodev2dev
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but it could be quite wrong.
In addition I have no idea how partial charges are computed.
2015-06-25 14:37 GMT-04:00 David van der Spoel sp...@xray.bmc.uu.se:
On 25/06/15 18:50, Nicolas Cheron wrote:
Hello,
I am wondering what is the status of GAFF in Open Babel? These two
pages http
Hi,
is it possible to generate a .xyz file from a Gaussian log file
containing frequency information, that has the dx dy dz fields?
jmol / jsmol can animate this so it would be cool for a website. However
jmol/jsmol can not read the freqencies directly from a .log file.
Thanks,
--
David van
On 2013-11-08 18:54, Geoffrey Hutchison wrote:
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
However even for good geometries OB has problems with bond orders
sometimes as I pointed out the other day. Is there anything that can be
done about that? Changing smiles?
Bond order
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Box 596, 75124
You probably have multiple pythons. Try to tell installation to use the new
one.
On 19 okt 2013, at 12:23, O. Baris Malcioglu baris.malcio...@gmail.com
wrote:
Hi everyone,
I have installed python3 to my Mac from the official distribution,
However, when I try to install openbabel with
On 2012-12-10 10:47, Chris Morley wrote:
On 09/12/2012 21:03, David van der Spoel wrote:
Thanks, I now use this which works:
if (conv.SetOutFormat(fpt))
{
conv.AddOption(f, OpenBabel::OBConversion::OUTOPTIONS,
FP4
On 2012-12-09 11:36, Chris Morley wrote:
On 08/12/2012 21:32, David van der Spoel wrote:
On 2012-12-08 17:42, Noel O'Boyle wrote:
C:\Users\Noelobabel -:c1(Br)cc(Br)ccc1 -ofpt -xf fp4 -xs
Arylbromide Aromatic
1 molecule converted
Great, I can reproduce that.
Is there a simple way
On 2012-12-09 22:14, Chris Swain wrote:
--
Message: 2
Date: Sat, 08 Dec 2012 14:51:44 +0100
From: David van der Spoel sp...@xray.bmc.uu.se
Subject: [Open Babel] substructure classification
To: openbabel-discuss@lists.sourceforge.net
Message-ID: 50c345f0.4070
compound
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
SMARTS_InteLigand.txt or copy it to your current directory and
edit it then.
- Noel
On 8 December 2012 13:51, David van der Spoel sp...@xray.bmc.uu.se wrote:
Hi,
is it possible with openbabel to classify a molecule based on substructures?
E.g.:
110-dichlorodecane.sdf
alkyl chloride
to openbabel.
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
to it. If I instead use the system-wide installed version
cmake-ing and linking works fine. Any clues to whether this could be due
to the above cmake code, the FindOpenBabel2.cmake or something else?
Thanks,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala
to be supported, including reading energy
terms etc.?
Thanks,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
On 2012-10-17 15:15, David van der Spoel wrote:
Hi,
I've done some G2 calculations on small molecules using Gaussian, and
each of these files contains 7 calculations. Babel crashes when trying
to read this:
% curl http://folding.bmc.uu.se/222-trichloroethanol-g2.log
222-trichloroethanol
On 17 okt 2012, at 21:30, Chris Morley c.mor...@gaseq.co.uk wrote:
On 17/10/2012 14:46, David van der Spoel wrote:
On 2012-10-17 15:15, David van der Spoel wrote:
Hi,
I've done some G2 calculations on small molecules using Gaussian, and
each of these files contains 7 calculations. Babel
xtc and
trr files.
ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.1.tar.gz
I guess this be incorporated into OB.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se
On 2012-10-08 21:08, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote:
On 2012-10-08 19:11, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote:
It adds TWO H for InChi output, not for SDF output, but it only produces
/newrelic-dev2dev
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On 2012-10-07 22:53, Reinis Danne wrote:
On Sun, Oct 07, 2012 at 10:06:57PM +0200, David van der Spoel wrote:
On 2012-10-07 21:28, Reinis Danne wrote:
On Sun, Oct 07, 2012 at 08:32:53PM +0200, David van der Spoel wrote:
On 2012-10-07 18:35, Reinis Danne wrote:
On Sun, Oct 07, 2012 at 11:20
On 2012-10-08 10:55, David van der Spoel wrote:
Hi,
To answer my own question: I now installed trunk, the development
version. The gaussian files now work fine, but the fulvene.pdb file
still gives problems:
% babel --version
No output file or format spec!
Open Babel 2.3.2 -- Oct 8 2012
On 2012-10-08 14:45, David van der Spoel wrote:
On 2012-10-08 10:55, David van der Spoel wrote:
Hi,
To answer my own question: I now installed trunk, the development
version. The gaussian files now work fine, but the fulvene.pdb file
still gives problems:
% babel --version
No output file
On 2012-10-08 19:11, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote:
On 2012-10-08 14:45, David van der Spoel wrote:
On 2012-10-08 10:55, David van der Spoel wrote:
Hi,
To answer my own question: I now installed trunk, the development
version
generation, since for many ions babel adds a proton where there
shouldn't be one (e.g. imidazolium and other ionic liquids, organic
cations).
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone
On 2012-10-07 18:35, Reinis Danne wrote:
On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote:
Hi,
when reading a gaussian output file the total charge is available and
that could be used to improve the bond order perception, alternatively
there could be a command line option
9 1.272 -0.893 1.269 1.00 0.00
H
HETATM 10 O MOL10 0.000 1.483 0.375 1.00 0.00
O
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp
On 2012-10-06 17:13, Reinis Danne wrote:
On Sat, Oct 06, 2012 at 01:06:51PM +0200, David van der Spoel wrote:
Hi,
I'm trying to implement an algorithm to determine bond orders into the
GROMACS MD package, and looked at the open babel version. There seems to
be a problem in the implementation
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