Hello
I have a question about find_pairs argument, angle. Especially when I'm
trying to find all hydrogen bonds with a script like this:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/list_hbonds.py
I'd like to know what angle is there? It is not very clear neither from
pymol documentation
GROMACS 5?
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in advance
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Hi
I can't get Bluetooth working on my Lenovo laptop, could you point me the
way to solve this problem please?
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1&iu=/4140/ostg.clktrk
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t;
>
>
>
>
> On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар
> wrote:
>
> > Hello, I've got a question. Is there a way to continue MD simulation, not
> > from last state but from specific time of MD? Say we have made a MD, have
> > analysed it and h
frame, make all minimisations etc.?
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or my
questions, but I'm quite novice in running gromacs on cluster.
2013/5/21 Justin Lemkul
>
>
> On 5/21/13 1:15 PM, Андрей Гончар wrote:
>
>> Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled
>> mdrun with MPI.
>> Now when I try
ss on cluster but
I see the opposite. What I'm doing wrong?
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statically linked instance of gromacs, copy it to another computer and use
it from my home directory.
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Open Babel 2.3.90 -- Mar 19 2012
2012/10/4 Fredrik Wallner :
> Hi,
>
> What version of Open Babel are you using?
>
> Kind regards,
> Fredrik
>
> 4 okt 2012 kl. 12:32 skrev Андрей Гончар :
>
>> Hi,
>>
>> I'm tryi
v
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Hello.
I have a question about a way to select a special chain in OBMolecule.
In the API documentation I found the way to retrieve an atom, a bond,
a residue but nothing about chains.
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Hello.
How to extract all low-energy conformations from MD-trajectory of protein?
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Hello. Is it possible to perform MD for protein-ligand interactions in
implicit water? And what about the precision of this kind of MD's? Are
they differ strong from these with explicit water?
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t to do molecular dynamics (MD) using gromacs of same ligand
> and binding site of my protein. Thats why i want to know how to place ligand
> in specific binding site and run MD using gromacs.
>
> Thanks,
> Nitin
>
>
> On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар wrote:
&
@gromacs.org.
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Hi all.
I'm trying to convert a pdb (PDB ID 1A94). In the beginning there are
2 ligangs with residue number 100 (named 0Q4) and chains A and E
accordingly. But after conversion by babel there is no more chain E
for residue 100, but there are 2 residues with id 100 and chain A.
In the HET section of
I found a solution!
With openbabel a pdb without residue names and numbers can be easily fixed:
1. babel file.pdb file.mol
2. babel file.mol file.pdb
Et voila! Now you have a pdb with repaired residue names!
2012/1/31 Андрей Гончар :
> Thanks!
>
> 2012/1/31 Thomas Holder :
>> I
Hi all!
I've just installed a new version of PyMol, but when I select a
repersentation different to the default, it displays a blank screen
and returns
unsupported IR in fragment shader 13
unsupported IR in fragment shader 13
unsupported IR in fragment shader 13
unsupported IR in fragment shader 1
Check the permissions on /dev/nvidia*
I had OpenMM, CUDA driver and gromacs installed, but I was unable to
run simulations on GPU until I've set permissions to 666
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Please se
gt; make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
>>> make: *** [mdrun] Error 2
>>>
>>> When I run make mdrun after deleting the 2 occurences of
>>> "-fexcess-precision=fast" from CMakeCache.txt the compilation works.
>>>
x-users
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gt;>> set_sequence CDEFGHIKL, myobj
>>>>
>>>> # update sequence viewer
>>>> rebuild
>>>>
>>>> Cheers,
>>>> Thomas
>>>>
>>>> On 01/30/2012 01:38 PM, gontchar andrey wrote:
>>>>>
>&g
Ok, thanks
2012/1/31 Mark Abraham :
> On 31/01/2012 7:14 PM, Андрей Гончар wrote:
>>
>> So for every residue I need to specify their atoms, am I right?
>
>
> Yeah. One way is to use make_ndx to select the atoms in the residues and
> make an index file group, then
So for every residue I need to specify their atoms, am I right?
2012/1/31 Mark Abraham :
> On 31/01/2012 7:06 PM, Андрей Гончар wrote:
>>
>> Hi!
>> Is it possible to specify which residues to restrain during MD simulation?
>> For example I have a protein, but I don
Hi!
Is it possible to specify which residues to restrain during MD simulation?
For example I have a protein, but I don't want to restrain all the
molecule, but a part.
How can I do this?
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Hi all
Do anybody know about the PyMol 1.5 release date?
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g
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solution is just do the bookkeeping yourself in the script.
>
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Oct 14, 2011 at 12:06 PM, Андрей Гончар wrote:
>> Hello.
>> As an example:
>> I create a chempy model
>> m = chempy.model.Indexed()
>> I add
an I want my model back. So I execute
m1 = cmd.get_model('loaded_model')
But now object m1 does not have the attribute 'name'
and m1.name gives an error.
Is it possible to add and preserve extra arguments to model objects?
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ists/listinfo/pymol-users
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>
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All the data continuously generated in your IT infrastructure contains a
definitive record of
er.
>
> Cheers,
>
> -- Jason
>
> On Fri, Sep 16, 2011 at 5:49 AM, Андрей Гончар wrote:
>> Hello!
>> Is there a way to combine two objects together?
>> Not just molecules bu
together?
2011/9/16 lina :
>
>
> On Fri, Sep 16, 2011 at 5:49 PM, Андрей Гончар wrote:
>>
>> Hello!
>> Is there a way to combine two objects together?
>> Not just molecules but a molecule and CGO object, for examlple?
>
> First, I don't understand well what
Hello!
Is there a way to combine two objects together?
Not just molecules but a molecule and CGO object, for examlple?
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ы японские сайты нормально корректно отображались.
>> Спасибо большое.
>>
>>
>
>
>
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cause pymol will only update the open GL display
> once the script terminates.
>
> Matthias
>
> On Wed, Sep 14, 2011 at 3:00 PM, Андрей Гончар wrote:
>> So what exactly do you want your script to do?
>> 1. Show loaded file
>> 2. Modify file
>> 3. Show modified
ipt.py gloabl" instead of "run script.py",
> followed by script("parameter1", "...")
>
> the openGL display still won't refresh?
>
> Best,
>
> Matthias
>
> On Wed, Sep 14, 2011 at 1:59 PM, Андрей Гончар wrote:
>> Try to do the
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Hi all! I have a question about wildcards usage in pymol.
For example if I want to delete all except obj1 I write:
delete not obj1
but this expression does not works as expected...
Is there a way in pymol to delete all except [something]?
In selections these experssions work. But in object names t
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что
> нажать.
>
>
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e48fcb2.7080...@korona-auto.com
>
>
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Archive:
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anks in advance.
>
>
>
> Smitty
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О да, это именно оно. Дело в том, что Cartoon - это вовсе не картон, а
скорее мультипликация
11 августа 2011 г. 9:49 пользователь Sergey Alyoshin
написал:
> 2011/8/11 Андрей Гончар :
>> Всем добрый день.
>> Сегодня во время работы с программой визуфлизации молекулярной графи
Всем добрый день.
Сегодня во время работы с программой визуфлизации молекулярной графики Avogadro
столкнулся с досадной ошибкой перевода. В стилях отображения в
оригинале среди прочего было Cartoon, переведено как "Картон".
Версия программы 1.0.1-3+b1, debian squeeze.
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I think so!
2011/7/8 Szilárd Páll :
> I think you made the right decision! :)
> --
> Szilárd
>
>
>
> On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote:
>> Thanks a lot!
>> Now we decided to use gromacs under linux and the installation of
>> gromacs an
BRARY_PATh in cygwin).
>
> As I did this >1 year ago the above might not be accurate and slight
> details might be missing. Let me know if you succeed.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар wrote:
>> Thank you
oth cmake and gcc
> is available for cygwin so you might be lucky and get mdrun-gpu
> compiled without any additional effort.
>
> All binaries on the Gromacs webpage _are outdated_ which is clearly
> stated on the respective page.
>
> Cheers,
> --
> Szilárd
>
>
&g
Hello! I have a misunderstood about the installation of gpu-enabled
gromacs under windows.
I'll try to explain: in system requirements of gromacs-gpu it is wrote
that Nvidia CUDA libraries have to be installed. But is it possible to
do under cygwin? This quertion appears because we run gromacs unde
elp
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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5 апреля 2011 г. 15:53 пользователь Max Kosmach написал:
> 05.04.2011 14:06, Андрей Гончар пишет:
>>
>> Добрый день. Перевод пятой части готов.
>>
>
>> #. type:
>> #: maint-guide.en.sgml:1831
>> msgid "Many dh_* commands invoked by the new dh
&g
Беру 5-й
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Krasnoselskaya str. 17, Moscow,
107140, Russia
http://i18n.counter.li.org/cgi-bin/certificate.cgi/499247>
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18 ноября 2010 г. 16:02 пользователь Peter Pentchev написал:
> On Thu, Nov 18, 2010 at 12:57:35PM +, James Brown wrote:
>> Peter Pentchev wrote:
>> > On Thu, Nov 18, 2010 at 12:12:00PM +, James Brown wrote:
>>
>> >
>> > Если фотографии в формате JPEG, тогда jpegtran из libjpeg-progs.
>> >
Добрый день.
Если кто может, поделитесь опытом установки Debian Squeeze на Compaq mini 110c?
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107140, Russi
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