Hydrogen@home, Проект исследования новых технологий производства и хранения водорода Налаштування

[nikelong]

Проект "Hydrogen@home"

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• Официальный сайт
• Официальная статистика по команде "Ukraine"
  
• Статистика на фришниках
• Статистика на фришниках по команде "Ukraine"
  
• Статус серверов проекта

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ТОП-20 участников:

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Дата основания команды - 31.03.2008 Капитан - Arbalet
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Для присоединения к команде Украины:
1. Загрузите BOINC менеджер (Если его у Вас еще нет!)
2. Перейдите в "расширенный вид"

3. Выберите сервис ---> добавить проект
4. Введите адрес проекта http://hydrogenathome.org/
5. Введите свои регистрационные данные.
6. Найдите нашу команду. Она называется Ukraine и адрес ее статистики вы могли видеть выше.
7. Если есть доступные для загрузки задания Вы их получите и начнете расчеты.
----------------------------------------------------------------------------------------------------------
Полезная информация:
Для идентификации пользователя в BOINC могут служить 2 вещи:
1) пара e-mail/пароль
2) межпроектный идентификационный ID (Cross-project ID) - 32значное шестнадцатиричное число.

Если Вы пожелаете подключится ещё и к другому BOINC-проекту, то помните: чтобы не плодить новых аккаунтов при подключении к новому проекту или команде, нужно обязательно везде регистрироваться с одним и тем же e-mail/паролем либо CPID. если при регистрации в проекте указать другие e-mail или пароль, BOINC создаст новый аккаунт с тем же именем!
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О проекте:
Проект исследования новых технологий производства и хранения водорода - экологически чистого вида топлива

• PDF-файл с описанием проекта

С оффсайта:
Our Research
Given the problems of Global Climate Change and Energy security, it makes sense to become energy independent with clean technologies.
Hydrogen@Home studies clean technologies for the production of hydrogen for energy purposes. Hydrogen used in fuel cell technologies has zero emissions of greenhouse gases. However, the most economical method of producing hydrogen (Methane Reformation) produces greenhouse gases.
Ideally, hydrogen from water has the potential to produce no greenhouse gases. One approach, is studying photo-biological systems to find highly efficient methods of producing hydrogen. Already researchers have identified photosynthetic bacteria capable of such reactions.
Hydrogen@Home attempts to predict previously uncharacterized catalytic interactions of biological catalysts. It attempts to find the most efficient method of producing hydrogen.
To achieve these goals, Hydrogen@Home simulates interactions of 3D structures of proteins and substrate. Structures are obtained from Research Collaboratory for Structural Bioinformatics (RCSB).
All Software used in this project is licensed under GPL.
Here is a paper describing initial graduate project that inspired this project. Datamining For Hydrogen Yielding Enzymes

Некоторые результаты:

• http://hydrogenathome.org/jmol-11.4.0/

Плюс, в новостях регулярно кидают линки на какую-либо тематическую литературу. В итоге, с информационной поддержкой у проекта нет проблем.

График ППД команды за последние 60 дней:

(Show/Hide)

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Статус сервера выдачи заданий:

http://wiki.bc-team.org/index.php?title=Hydrogen%40home/en

https://distributed.ru/wiki/pro:hydrogen

http://www.boinc-af.org/content/view/587/217/

http://www.dp.by/wiki/Projects/Hydrogenathome

Це повідомлення відредагував Death: May 1 2009, 22:20

[Death]

делись )))))

[Rilian]

Ок, сегодня сикретне инвайте получил

[Rilian]

ПОШЛА ЖАРА!!!!!!!11111111111

мне попалась одна ВЮ - 40 секунд, 0.20 очков

больше ВЮ нет

<core_client_version>6.4.5</core_client_version>
<![CDATA[
<stderr_txt>
wrapper: starting
wrapper: running ../../projects/hydrogenathome.org/unzip_1.19_windows_intelx86.exe (-qq -n gromacs.zip)
wrapper: running gromacs/bin/pdb2gmx.exe (-ff amber03 -water tip4p -o conf.gro)
:-) G R O M A C S (-:

Gromacs Runs One Microsecond At Cannonball Speeds

:-) VERSION 4.0.3 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) gromacs/bin/pdb2gmx (-:

Option Filename Type Description
------------------------------------------------------------
-f eiwit.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-o conf.gro Output Structure file: gro g96 pdb
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]merge bool no Merge chains into one molecule definition
-ff string amber03 Force field, interactive by default. Use -h for
information.
-water enum tip4p Water model to use: with GROMOS we recommend SPC,
with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p
or f3c
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine selection, iso charged
-[no]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
-[no]gln bool no Interactive Glutamine selection, iso neutral
-[no]his bool no Interactive Histidine selection, iso checking
H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
Phenylalanine, Tryptophane and Tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu

Opening library file ffamber03.rtp
Opening library file aminoacids.dat
Opening library file aminoacids.dat
Opening library file atommass.dat
Opening library file vdwradii.dat
Opening library file dgsolv.dat
Opening library file electroneg.dat
Opening library file elements.dat
Opening library file xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
WARNING: there were 1851 atoms with zero occupancy and 16 atoms with
occupancy unequal to one (out of 1868 atoms). Check your pdb file.
Opening library file ffamber03.atp

Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
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Atomtype 1
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Atomtype 1
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Atomtype 1
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Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Opening library file ffamber03.rtp

Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
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Residue 122
Residue 123
Residue 124
Residue 125
Residue 126
Residue 127
Residue 128
Residue 129
Residue 130
Residue 131
Sorting it all out...
Opening library file ffamber03.hdb
Opening library file ffamber03-n.tdb
Opening library file ffamber03-c.tdb
There are 342 donors and 342 acceptors
There are 427 hydrogen bonds
Opening library file specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
MET22 MET60 MET90 MET142 MET180
SD168 SD469 SD695 SD1101 SD1402
MET60 SD469 1.198
MET90 SD695 2.273 1.291
MET142 SD1101 3.755 3.577 4.559
MET180 SD1402 3.688 3.217 3.924 1.222
MET210 SD1628 4.989 4.300 4.652 2.507 1.520
Making bonds...
Warning: Long Bond (1-5 = 0.458477 nm)
Warning: Long Bond (5-7 = 0.365351 nm)
Warning: Long Bond (5-18 = 0.286245 nm)
Warning: Long Bond (7-10 = 0.250088 nm)
Warning: Long Bond (10-11 = 0.510701 nm)
Warning: Long Bond (10-16 = 0.583405 nm)
Warning: Long Bond (11-12 = 0.951967 nm)
Warning: Long Bond (14-16 = 0.336489 nm)
Warning: Long Bond (18-19 = 0.330189 nm)
Warning: Long Bond (18-20 = 8.76171 nm)
Warning: Long Bond (18-20 = 8.76171 nm)
Warning: Short Bond (281-282 = 0.0173118 nm)
Warning: Short Bond (1223-1224 = 0.03919 nm)
Warning: Long Bond (1836-1840 = 0.375255 nm)
Warning: Long Bond (1840-1842 = 0.565792 nm)
Warning: Long Bond (1840-1853 = 0.608461 nm)
Warning: Long Bond (1842-1845 = 0.300082 nm)
Warning: Long Bond (1845-1846 = 1.06587 nm)
Warning: Long Bond (1845-1851 = 0.809173 nm)
Warning: Long Bond (1846-1847 = 0.905759 nm)
Warning: Long Bond (1847-1849 = 0.422019 nm)
Warning: Long Bond (1849-1851 = 0.501367 nm)
Warning: Long Bond (1853-1854 = 0.675574 nm)
Warning: Long Bond (1853-1855 = 7.24217 nm)
Warning: Long Bond (1853-1855 = 7.24217 nm)
Warning: Short Bond (3309-3310 = 0.0469252 nm)
Warning: Short Bond (3309-3311 = 0.0473808 nm)
Warning: Short Bond (3441-3442 = 0.0498146 nm)
Warning: Short Bond (3441-3443 = 0.0371581 nm)
Opening library file aminoacids.dat
Number of bonds was 3720, now 3718
Generating angles, dihedrals and pairs...
Before cleaning: 9746 pairs
Before cleaning: 9886 dihedrals
Keeping all generated dihedrals
There are 9886 dihedrals, 745 impropers, 6740 angles
9680 pairs, 3718 bonds and 0 virtual sites
Total mass 26734.992 a.m.u.
Total charge -4.000 e
Writing topology

Writing coordinate file...
wrapper: running gromacs/bin/grompp.exe (-f grompp_min.mdp -c conf.gro)
Option Filename Type Description
------------------------------------------------------------
-f grompp_min.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'

NOTE 1 [file topol.top, line 34498]:
System has non-zero total charge: -4.000002e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file aminoacids.dat
Making dummy/rest group for T-Coupling containing 3670 elements
Making dummy/rest group for Acceleration containing 3670 elements
Making dummy/rest group for Freeze containing 3670 elements
Making dummy/rest group for VCM containing 3670 elements
Number of degrees of freedom in T-Coupling group rest is 11007.00
Making dummy/rest group for User1 containing 3670 elements
Making dummy/rest group for User2 containing 3670 elements
Making dummy/rest group for Or. Res. Fit containing 3670 elements
Making dummy/rest group for QMMM containing 3670 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): Protein
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): Protein
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file grompp_min.mdp, line unknown]:
You are using a plain Coulomb cut-off, this will often produce artifacts.
You might want to consider using PME electrostatics.


writing run input file...

There were 2 notes

gcq#185: "It is Lunchtime" (A.R. Van Buuren)

wrapper: running gromacs/bin/mdrun.exe ()
:-) G R O M A C S (-:

Great Red Owns Many ACres of Sand

:-) VERSION 4.0.3 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) gromacs/bin/mdrun (-:

Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Run input file: tpr tpb tpa
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c confout.gro Output Structure file: gro g96 pdb
-e ener.edr Output Energy file: edr ene
-g md.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool yes Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]append bool no Append to previous output files when restarting
from checkpoint
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system

Reading file topol.tpr, VERSION 4.0.3 (single precision)
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 2000
Warning: 1-4 interaction between 1 and 20 at distance 8.662 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 550 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 7.3886250e+04
Maximum force = 3.1850342e+03 on atom 2895
Norm of force = 3.1263608e+02

gcq#151: "I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart)

called boinc_finish

</stderr_txt>
]]>

[Death]

не успел.

6611 не просит задания. альмер работал. (((

[Rilian]

с утра in progress было 17 заданий - сейчас 147. Значит они раздаются по чуть-чуть маленькими порциями. Пробуйте..

[Rilian]

За сегодня поймал 5 ВЮ по 0.7 очков каждая!

[Rilian]

КОму надо инвайт - пишите в личку!

[(_KoDAk_)]

March 7, 2009

We are searching for sample molecular visualization code to write a screensaver or interactive client. Specifically we would like some code written in C++ using OpenGL and ready to compile in Visual Studio but Cygwin may be sufficient.

[Rilian]

Пошли задания с автодоком, считаются по 20 минут, дают по 7 очков

[Rilian]

Мы уже на 68 месте!

http://hydrogenathome.org/top_teams.php?so...redit&offset=60

А также на 7 месте по скорости

http://hydrogenathome.org/top_teams.php?so...y=expavg_credit

[Rilian]

Death, приветствуем в команде!

Мы уже на 66 месте!

http://hydrogenathome.org/top_teams.php?so...redit&offset=60

А также на 12 месте по скорости

http://hydrogenathome.org/top_teams.php?so...y=expavg_credit

[Death]

я скачал ВУ из интернета, она мне оказалась не нужна, как мне закачать её обратно?

Results ready to send 0
Results in progress 31,293
Workunits waiting for validation 0
Workunits waiting for assimilation 0
Workunits waiting for deletion 0
Results waiting for deletion 0
Transitioner backlog (hours) 1

01.05.2009 23:15:54 Hydrogen@Home [error] Error reported by file upload server: Server is out of disk space

ещё 7500 вёдер, почтеннейший...

40 42 XtremeSystems 50 50 42 0 8 103 933 21 3,562
41 43 HUNGARY - HAJRA MAGYARORSZAG! HAJRA MAGYAROK! 29 29 38 6 7 79 111 8 3,455
42 44 1 GOUSA 352 352 490 0 70 844 2,262 95 3,319
43 45 1 boinc@italy 109 109 59 0 9 170 356 18 3,202
44 46 2 Atlantis Base 387 387 498 0 71 886 1,595 89 2,978
45 47 1 TEAMgsvr 0 0 0 0 0 0 0 0 2,820
46 48 4 Ei ydinvoimaa - No Nuclear Power 367 367 251 0 36 618 2,232 80 2,766
47 49 2 University of West Bohemia 0 0 0 0 0 0 274 6 2,660
48 50 1 Calm Chaos 13 13 111 15 23 171 2,017 41 2,578
49 51 Ukraine 48 48 42 0 6 90 1,186 25 2,547

ещё 1к очей и +10 мест )))

[nikelong]

я скачал ВУ из интернета, она мне оказалась не нужна, как мне закачать её обратно?

Наверно нажать кнопочку "прервать обработку"

[Death]

nikelong, ты не врубился чувак.

01.05.2009 23:15:54 Hydrogen@Home [error] Error reported by file upload server: Server is out of disk space

[vitalidze1]

пАхоже, шо бобік здох. Не шле нових розрахунків.