From owner-chemistry@ccl.net Wed May 20 00:05:01 2015 From: "Lela Vukovic Lvukov1/a\illinois.edu" To: CCL Subject: CCL: Workshop on Computational Biophysics (Berkeley, Aug 3-7, 2015) Message-Id: <-51385-150519235413-9829-9gb7/NdBnW6V+dBNkavomg/a\server.ccl.net> X-Original-From: "Lela Vukovic" Date: Tue, 19 May 2015 23:54:11 -0400 Sent to CCL by: "Lela Vukovic" [Lvukov1(~)illinois.edu] The Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/ to be held August 3-7, 2015 at the University of California Berkeley. Application, selection, and notification of participants is on-going through July 15, 2015. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies, and will cover the following topics: using the biophysics software VMD and NAMD, applications of VMD and NAMD in modern research, force fields and parameterizing new molecules, modeling nucleic acid systems, computational nano-bio, molecular dynamics flexible fitting of structures into cryo electron microscopy maps, and refinement of low resolution crystal structures. Relevant physical concepts, mathematical techniques, and computational methods will be introduced. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 24 participants. The workshop will be held August 3-7, 2015. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Course materials will be provided. The workshop is sponsored by the National Institute of General Medical Sciences (www.nigms.nih.gov) and the NIH Center for Macromolecular Modeling and Bioinformatics. We look forward to receiving your application! TCBG Workshop Organizers Email: workshop+berkeley2015*|*ks.uiuc.edu From owner-chemistry@ccl.net Wed May 20 13:51:01 2015 From: "Partha Sengupta anapspsmo*_*gmail.com" To: CCL Subject: CCL: free pymol for windows 7 32 bit for docking and Molecular mechanics Message-Id: <-51386-150520131204-27183-mkdTDpJ+yx3AP29l7XFeTQ#%#server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a11c3f56c595928051686865b Date: Wed, 20 May 2015 22:41:58 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo : gmail.com] --001a11c3f56c595928051686865b Content-Type: text/plain; charset=UTF-8 Friends, I want to dock a ligand type molecule with a protein by free "Pymol" software. But I am unable to download the "pymol for windows7 32 bit". How to use it? Please help Partha -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a11c3f56c595928051686865b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Friends, I want to dock a ligand type molecule with a prot= ein by free "Pymol" software. But I am unable to download the &qu= ot;pymol for windows7 32 bit". How to use it? Please help
Partha
--
Dr. Partha Sara= thi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--001a11c3f56c595928051686865b-- From owner-chemistry@ccl.net Wed May 20 15:56:00 2015 From: "Billy McCann thebillywayne_+_gmail.com" To: CCL Subject: CCL: Workshop on Computational Biophysics (Berkeley, Aug 3-7, 2015) Message-Id: <-51387-150520144459-31556-r3mbaxFFHjL9cEAd5MxYFA^server.ccl.net> X-Original-From: Billy McCann Content-Type: text/plain; charset=UTF-8 Date: Wed, 20 May 2015 14:44:38 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne[A]gmail.com] Hello. This looks like a very exciting opportunity. If you would indulge me, I have a few words. One item in particular about this workshop is somewhat unfortunate for me, that is, the laptop hardware requirements. The workshop requires participants to bring their own laptop. This is understandable. The hardware requirements for the laptop requires a discrete GPU. This also is understandable. However, such laptops do not come cheaply. I grant that the specifications listed represent technology that is more than a decade old. Perhaps an older, inexpensive laptop with these specs or better could be bought from ebay or craigslist? These sites are patronized for technology with "caveat emptor" writ large. This requirement alone keeps me from even applying. I, like many other chemists at the beginning of their scientific careers, am competing with an ever increasing number of colleagues for very few available positions and grant money that shrinks year by year. Some of us simply won't make it. Fact. You are holding this workshop in August, a time approximately when some of us are facing the end of our contracts and whose future employment is still dubious. The acquisition of laptops with a discrete GPU (sometimes referred to as "gaming laptops") will probably take priority far below the securing of food, shelter, clothing, and medicine. I apologize for the rant. But certain aspects of remaining competitive in computational chemistry simply strike an all-too-sensitive nerve for me. Perhaps I'm over reacting. Perhaps it's that I'm frustrated at the state of job seeking in chemistry. Perhaps I'm frustrated because of the frequency at which I'm advertised such workshops, workshops that I would love to attend and that I know would help me progress towards my long-term scientific goals (yours in particular does), but the limiting reagent in the reaction is money. Always money. This ends my words. I may be alone in the sentiments that I've expressed here. But I have a hunch that I'm not alone. For your consideration, Billy Wayne McCann, Ph.D. -- Billy Wayne McCann, Ph.D. irc://irc.freenode.net:bwayne Plays, farces, spectacles, gladiators, strange beasts, medals, pictures, and other such opiates, these were for ancient peoples the bait toward slavery, the price of their liberty, the instruments of tyranny. By these practices and enticements the ancient dictators so successfully lulled their subjects under the yoke, that the stupefied peoples, fascinated by the pastimes and vain pleasures flashed before their eyes, learned subservience as naively, but not so creditably, as little children learn to read by looking at bright picture books. Roman tyrants invented a further refinement. They often provided the city wards with feasts to cajole the rabble, always more readily tempted by the pleasure of eating than by anything else. The most intelligent and understanding amongst them would not have quit his soup bowl to recover the liberty of the Republic of Plato. Tyrants would distribute largess, a bushel of wheat, a gallon of wine, and a sesterce: and then everybody would shamelessly cry, 'Long live the King!' The fools did not realize that they were merely recovering a portion of their own property, and that their ruler could not have given them what they were receiving without having first taken it from them. ~Juvenal On Tue, May 19, 2015 at 11:54 PM, Lela Vukovic Lvukov1/aillinois.edu wrote: > > Sent to CCL by: "Lela Vukovic" [Lvukov1(~)illinois.edu] > The Theoretical and Computational Biophysics Group, NIH Resource for > Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the > University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a > > "Hands-On" Workshop on Computational Biophysics > > http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/ > > to be held August 3-7, 2015 at the University of California Berkeley. Application, selection, and > notification of participants is on-going through July 15, 2015. > > The workshop will explore physical models and computational approaches used for the > simulation of biological systems and the investigation of their function at an atomic level. The > course will be based on case studies, and will cover the following topics: using the biophysics > software VMD and NAMD, applications of VMD and NAMD in modern research, force fields > and parameterizing new molecules, modeling nucleic acid systems, computational nano-bio, > molecular dynamics flexible fitting of structures into cryo electron microscopy maps, and > refinement of low resolution crystal structures. Relevant physical concepts, mathematical > techniques, and computational methods will be introduced. > > The workshop is designed for graduate students and postdoctoral researchers in > computational and/or biophysical fields who seek to extend their research skills to include > computational and theoretical expertise, as well as other researchers interested in theoretical > and computational biophysics. Theory sessions in the morning will be followed by hands-on > computer labs in the afternoon in which students will be able to set up and run simulations. > Enrollment limited to 24 participants. The workshop will be held August 3-7, 2015. All > participants are required to bring their own laptop, prepared for use in workshop tutorial > sessions. Course materials will be provided. > > The workshop is sponsored by the National Institute of General Medical Sciences > (www.nigms.nih.gov) and the NIH Center for Macromolecular Modeling and Bioinformatics. > > We look forward to receiving your application! > > TCBG Workshop Organizers > Email: workshop+berkeley2015^-^ks.uiuc.edu> > From owner-chemistry@ccl.net Wed May 20 20:01:00 2015 From: "Kristopher Keipert kwk:-:iastate.edu" To: CCL Subject: CCL: Workshop on Computational Biophysics (Berkeley, Aug 3-7, 2015) Message-Id: <-51388-150520173735-31801-shn1WVv5LRtHbWP3Y6hJMw_+_server.ccl.net> X-Original-From: Kristopher Keipert Content-Type: multipart/alternative; boundary=047d7b6732bad8878e05168a3ba2 Date: Wed, 20 May 2015 16:36:48 -0500 MIME-Version: 1.0 Sent to CCL by: Kristopher Keipert [kwk!=!iastate.edu] --047d7b6732bad8878e05168a3ba2 Content-Type: text/plain; charset=UTF-8 Are you sure a discrete graphics card is required? "Graphics card: nVidia Geforce Ti4600, or comparable" The integrated graphics offerings from AMD and Intel have surpassed the performance of the Ti4600 for at least 5 years and definitely meet the minimum requirements from a performance standpoint. It looks like they're suggesting minimum hardware requirements to run VMD and NAMD, which is easy enough to test. On Wed, May 20, 2015 at 1:44 PM, Billy McCann thebillywayne_+_gmail.com < owner-chemistry!=!ccl.net> wrote: > > Sent to CCL by: Billy McCann [thebillywayne[A]gmail.com] > Hello. > > This looks like a very exciting opportunity. > > If you would indulge me, I have a few words. > > One item in particular about this workshop is somewhat unfortunate for > me, that is, the laptop hardware requirements. > > The workshop requires participants to bring their own laptop. This is > understandable. The hardware requirements for the laptop requires a > discrete GPU. This also is understandable. However, such laptops do > not come cheaply. > > I grant that the specifications listed represent technology that is > more than a decade old. Perhaps an older, inexpensive laptop with > these specs or better could be bought from ebay or craigslist? These > sites are patronized for technology with "caveat emptor" writ large. > > This requirement alone keeps me from even applying. > > I, like many other chemists at the beginning of their scientific > careers, am competing with an ever increasing number of colleagues for > very few available positions and grant money that shrinks year by > year. Some of us simply won't make it. Fact. You are holding this > workshop in August, a time approximately when some of us are facing > the end of our contracts and whose future employment is still dubious. > The acquisition of laptops with a discrete GPU (sometimes referred to > as "gaming laptops") will probably take priority far below the > securing of food, shelter, clothing, and medicine. > > I apologize for the rant. But certain aspects of remaining competitive > in computational chemistry simply strike an all-too-sensitive nerve > for me. Perhaps I'm over reacting. Perhaps it's that I'm frustrated > at the state of job seeking in chemistry. Perhaps I'm frustrated > because of the frequency at which I'm advertised such workshops, > workshops that I would love to attend and that I know would help me > progress towards my long-term scientific goals (yours in particular > does), but the limiting reagent in the reaction is money. Always > money. > > This ends my words. I may be alone in the sentiments that I've > expressed here. But I have a hunch that I'm not alone. > > > For your consideration, > > Billy Wayne McCann, Ph.D. > > > -- > Billy Wayne McCann, Ph.D. > irc://irc.freenode.net:bwayne > > Plays, farces, spectacles, gladiators, strange beasts, medals, > pictures, and other such opiates, these were for ancient peoples the > bait toward slavery, the price of their liberty, the instruments of > tyranny. By these practices and enticements the ancient dictators so > successfully lulled their subjects under the yoke, that the stupefied > peoples, fascinated by the pastimes and vain pleasures flashed before > their eyes, learned subservience as naively, but not so creditably, as > little children learn to read by looking at bright picture books. > Roman tyrants invented a further refinement. They often provided the > city wards with feasts to cajole the rabble, always more readily > tempted by the pleasure of eating than by anything else. The most > intelligent and understanding amongst them would not have quit his > soup bowl to recover the liberty of the Republic of Plato. Tyrants > would distribute largess, a bushel of wheat, a gallon of wine, and a > sesterce: and then everybody would shamelessly cry, 'Long live the > King!' The fools did not realize that they were merely recovering a > portion of their own property, and that their ruler could not have > given them what they were receiving without having first taken it from > them. > ~Juvenal > > > > > On Tue, May 19, 2015 at 11:54 PM, Lela Vukovic Lvukov1/aillinois.edu > wrote: > > > > Sent to CCL by: "Lela Vukovic" [Lvukov1(~)illinois.edu] > > The Theoretical and Computational Biophysics Group, NIH Resource for > > Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the > > University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a > > > > "Hands-On" Workshop on Computational Biophysics > > > > http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/ > > > > to be held August 3-7, 2015 at the University of California Berkeley. > Application, selection, and > > notification of participants is on-going through July 15, 2015. > > > > The workshop will explore physical models and computational approaches > used for the > > simulation of biological systems and the investigation of their function > at an atomic level. The > > course will be based on case studies, and will cover the following > topics: using the biophysics > > software VMD and NAMD, applications of VMD and NAMD in modern research, > force fields > > and parameterizing new molecules, modeling nucleic acid systems, > computational nano-bio, > > molecular dynamics flexible fitting of structures into cryo electron > microscopy maps, and > > refinement of low resolution crystal structures. Relevant physical > concepts, mathematical > > techniques, and computational methods will be introduced. > > > > The workshop is designed for graduate students and postdoctoral > researchers in > > computational and/or biophysical fields who seek to extend their > research skills to include > > computational and theoretical expertise, as well as other researchers > interested in theoretical > > and computational biophysics. Theory sessions in the morning will be > followed by hands-on > > computer labs in the afternoon in which students will be able to set up > and run simulations. > > Enrollment limited to 24 participants. The workshop will be held August > 3-7, 2015. All > > participants are required to bring their own laptop, prepared for use in > workshop tutorial > > sessions. Course materials will be provided. > > > > The workshop is sponsored by the National Institute of General Medical > Sciences > > (www.nigms.nih.gov) and the NIH Center for Macromolecular Modeling and > Bioinformatics. > > > > We look forward to receiving your application! > > > > TCBG Workshop Organizers > > Email: workshop+berkeley2015^-^ks.uiuc.edu> > > --047d7b6732bad8878e05168a3ba2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Are you sure a discrete graphics card is require= d?

"Graphics card: nVidia Geforce Ti4600, or compara= ble"

The integrated graphics offerings from AMD and = Intel have surpassed the performance of the Ti4600 for at least 5 years and= definitely meet the minimum requirements from a performance standpoint. It= looks like they're suggesting minimum hardware requirements to run VMD= and NAMD, which is easy enough to test.=C2=A0



On W= ed, May 20, 2015 at 1:44 PM, Billy McCann thebillywayne_+_gmail.com <owner-chemistry!=!ccl.net> wr= ote:

Sent to CCL by: Billy McCann [thebillywayne[A]gmail.com]
Hello.

This looks like a very exciting opportunity.

If you would indulge me, I have a few words.

One item in particular about this workshop is somewhat unfortunate for
me, that is, the laptop hardware requirements.

The workshop requires participants to bring their own laptop. This is
understandable.=C2=A0 The hardware requirements for the laptop requires a discrete GPU. This also is understandable. However, such laptops do
not come cheaply.

I grant that the specifications listed represent technology that is
more than a decade old. Perhaps an older, inexpensive laptop with
these specs or better could be bought from ebay or craigslist? These
sites are patronized for technology with "caveat emptor" writ lar= ge.

This requirement alone keeps me from even applying.

I, like many other chemists at the beginning of their scientific
careers, am competing with an ever increasing number of colleagues for
very few available positions and grant money that shrinks year by
year. Some of us simply won't make it. Fact. You are holding this
workshop in August, a time approximately when some of us are facing
the end of our contracts and whose future employment is still dubious.
The acquisition of laptops with a discrete GPU (sometimes referred to
as "gaming laptops") will probably take priority far below the securing of food, shelter, clothing, and medicine.

I apologize for the rant. But certain aspects of remaining competitive
in computational chemistry simply strike an all-too-sensitive nerve
for me.=C2=A0 Perhaps I'm over reacting. Perhaps it's that I'm = frustrated
at the state of job seeking in chemistry. Perhaps I'm frustrated
because of the frequency at which I'm advertised such workshops,
workshops=C2=A0 that I would love to attend and that I know would help me progress towards my long-term scientific goals (yours in particular
does), but the limiting reagent in the reaction is money.=C2=A0 Always
money.

This ends my words. I may be alone in the sentiments that I've
expressed here.=C2=A0 But I have a hunch that I'm not alone.


For your consideration,

Billy Wayne McCann, Ph.D.


--
Billy Wayne McCann, Ph.D.
irc://irc.freenode.net:bwayne

Plays, farces, spectacles, gladiators, strange beasts, medals,
pictures, and other such opiates, these were for ancient peoples the
bait toward slavery, the price of their liberty, the instruments of
tyranny. By these practices and enticements the ancient dictators so
successfully lulled their subjects under the yoke, that the stupefied
peoples, fascinated by the pastimes and vain pleasures flashed before
their eyes, learned subservience as naively, but not so creditably, as
little children learn to read by looking at bright picture books.
Roman tyrants invented a further refinement. They often provided the
city wards with feasts to cajole the rabble, always more readily
tempted by the pleasure of eating than by anything else. The most
intelligent and understanding amongst them would not have quit his
soup bowl to recover the liberty of the Republic of Plato. Tyrants
would distribute largess, a bushel of wheat, a gallon of wine, and a
sesterce: and then everybody would shamelessly cry, 'Long live the
King!' The fools did not realize that they were merely recovering a
portion of their own property, and that their ruler could not have
given them what they were receiving without having first taken it from
them.
~Juvenal




On Tue, May 19, 2015 at 11:54 PM, Lela Vukovic Lvukov1/aillinois.edu
<owner-chemistry%a%ccl.net<= /a>> wrote:
>
> Sent to CCL by: "Lela=C2=A0 Vukovic" [Lvukov1(~)illinois.edu]
> The Theoretical and Computational Biophysics Group, NIH Resource for > Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the
> University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a
>
>=C2=A0 "Hands-On" Workshop on Computational Biophysics
>
> http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/ >
> to be held August 3-7, 2015 at the University of California Berkeley. = Application, selection, and
> notification of participants is on-going through July 15, 2015.
>
> The workshop will explore physical models and computational approaches= used for the
> simulation of biological systems and the investigation of their functi= on at an atomic level. The
> course will be based on case studies, and will cover the following top= ics: using the biophysics
> software VMD and NAMD, applications of VMD and NAMD in modern research= , force fields
> and parameterizing new molecules, modeling nucleic acid systems, compu= tational nano-bio,
> molecular dynamics flexible fitting of structures into cryo electron m= icroscopy maps, and
> refinement of low resolution crystal structures. Relevant physical con= cepts, mathematical
> techniques, and computational methods will be introduced.
>
> The workshop is designed for graduate students and postdoctoral resear= chers in
> computational and/or biophysical fields who seek to extend their resea= rch skills to include
> computational and theoretical expertise, as well as other researchers = interested in theoretical
> and computational biophysics. Theory sessions in the morning will be f= ollowed by hands-on
> computer labs in the afternoon in which students will be able to set u= p and run simulations.
> Enrollment limited to 24 participants. The workshop will be held Augus= t 3-7, 2015. All
> participants are required to bring their own laptop, prepared for use = in workshop tutorial
> sessions. Course materials will be provided.
>
> The workshop is sponsored by the National Institute of General Medical= Sciences
> (www.nigms.nih.= gov) and the NIH Center for Macromolecular Modeling and Bioinformatics.=
>
> We look forward to receiving your application!
>
> TCBG Workshop Organizers
> Email: workshop+berkeley2015^-^ks.uiuc.edu>
>



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--047d7b6732bad8878e05168a3ba2-- From owner-chemistry@ccl.net Wed May 20 23:13:01 2015 From: "Billy McCann thebillywayne:+:gmail.com" To: CCL Subject: CCL: Workshop on Computational Biophysics (Berkeley, Aug 3-7, 2015) Message-Id: <-51389-150520223911-11663-YCv88VTjz2c3y7n2pwhYDA]![server.ccl.net> X-Original-From: Billy McCann Content-Type: text/plain; charset=UTF-8 Date: Thu, 21 May 2015 02:38:50 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne]~[gmail.com] > Are you sure a discrete graphics card is required? That they specify a "graphics card" and not a "graphical processing unit" indicates, to me, that this workshop requires a laptop with a *discrete* graphics card and not an integrated graphics solution. Also the specific brand mentioned, nVidia, supplies *solely* discrete graphics solutions in consumer grade laptops. Also, consider the advice given regarding the Mac platform: "Macintosh computers often come with sufficient graphics processing power, so no additional card is necessary." By inference, non-Macintosh computers *will* need an additional card. Overall, reading the laptop requirements page leaves me somewhat confused. (".... up-to-date hardware, operating systems, and software versions .... Windows 2000, Max OS X 10.3 ... G4 ... Pentium 4 ..." ???) But I'm at least going to give the people coordinating a computational biophysics workshop the benefit of the doubt that they know the difference between a "graphics card" and an intel or amd integrated graphics processing unit. You know, I'm probably getting worked up over nothing, honestly. Everything costs money, I suppose. https://www.youtube.com/watch?v=-0kcet4aPpQ I think this one probably got to me a bit more than usual because of how badly I want to get into this field. It's the next logical step in what I want to accomplish in the long run. It's probably best that I slink away and get back to writing resumes. I hope the workshop is a great success. Regards, BW