From owner-chemistry@ccl.net Wed Jun 11 09:05:01 2008 From: "Zsolt Zsoldos zsolt(~)simbiosys.ca" To: CCL Subject: CCL: recommendation for workstation purchase Message-Id: <-37135-080610230505-21909-cGGj1xLM/NMeE68txuzLNg::server.ccl.net> X-Original-From: "Zsolt Zsoldos" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 10 Jun 2008 22:07:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Zsolt Zsoldos" [zsolt * simbiosys.ca] Rachelle, If you are looking for pre-built complete systems with good quality parts and full linux compatibility and support, then I recommend you to look at this company: http://www.aslab.com/ I have been ordering various machines from them for the last 10 years and they work well, even today we are still running the first dual P3 system we bought from them in 1998 (although it has been downgraded > from workstation to web server by now). Best regards, Zsolt Zsoldos http://www.simbiosys.ca/ On Tue, Jun 10, 2008 at 6:13 PM, Kalju Kahn kalju()chem.ucsb.edu wrote: > > Sent to CCL by: "Kalju Kahn" [kalju[a]chem.ucsb.edu] > Rachelle, > > Are you thinking of self-assembly or a prebuilt machine? I have been > happy with self-built machines around Gigabyte or Abit motherboards based > on Intel P35 or X38 chipsets stuffed with 6-8 GB of DDR2 memory. > Processors like E8400 or Q9300 are affordable and sufficient for what you > describe. > > If you are thinking of stereo, Quadro FX1400 (128 MB RAM) performs OK for > small proteins ... it is old technology but newer stereo-enabled cards > (Quadro 3500 Quadro 3700) are rather expensive. FX1400 runs nicely on > CentOS, and supports dual monitors (consider CRT for full-screen > visualization + LCD for concurrent text work) > > Best luck, > > Kalju > >> >> Sent to CCL by: "Rachelle Joyce Bienstock" [biensto1(0)niehs.nih.gov] >> >> Hi: >> >> I am looking to purchase a dual processor workstation to do >> some homology modeling and run small MD simulations (AMBER,CHARMM, NAMD) >> and >> commercial Schrodinger and Accelrys software packages, and to use >> to set up jobs to be exported to a big cluster, as well as view results >> for visualization... with a >> high-end good graphics card, running Linux Centos 5 and I was looking >> for recommendations on which processors,which vendors and which >> machines... >> >> Thanks, Rachelle> >> >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106> > > From owner-chemistry@ccl.net Wed Jun 11 10:06:00 2008 From: "sudipta sinha sudipta.mml]*[gmail.com" To: CCL Subject: CCL: REading .dcd file by fortran program Message-Id: <-37136-080610154719-26071-r0WtUc0cu3KQJ0sCan23UQ,+,server.ccl.net> X-Original-From: "sudipta sinha" Content-Type: multipart/alternative; boundary="----=_Part_21134_33553692.1213123773585" Date: Wed, 11 Jun 2008 00:19:33 +0530 MIME-Version: 1.0 Sent to CCL by: "sudipta sinha" [sudipta.mml!^!gmail.com] ------=_Part_21134_33553692.1213123773585 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi All, I am using NAMD software for MD simulation of a protein. The output coordinate files are .dcd. I want to read this file by fortran code. Is it possible? If so how I will do that. If anybody gives any sample code for reading reading that specific file. It will very helpful to me. Thanks and regards Sudipta ------=_Part_21134_33553692.1213123773585 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi All,

        I am using NAMD software for MD simulation of a protein. The output coordinate files are .dcd.  I want  to read  this file  by fortran code.  Is  it  possible? If so how I will do that. If anybody gives any sample code for reading reading that specific file.  It  will very  helpful to me.

Thanks and regards
Sudipta
------=_Part_21134_33553692.1213123773585-- From owner-chemistry@ccl.net Wed Jun 11 12:22:00 2008 From: "Ramon Crehuet rcsqtc:iiqab.csic.es" To: CCL Subject: CCL: REading .dcd file by fortran program Message-Id: <-37137-080611121320-7520-R0KHU4pzMwOlgk/OYlGfDA!=!server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 11 Jun 2008 17:14:26 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc|*|iiqab.csic.es] Hi Sudipta, You can check the Dynamo library of subroutines. The older version is in Fortran 90 (the newer in python) and has subroutines for reading and writing dcd files. You can use the subroutine or see how it is done in the source code. http://www.pdynamo.org/mainpages/ Cheers, Ramon sudipta sinha sudipta.mml]*[gmail.com wrote: > Hi All, > > I am using NAMD software for MD simulation of a protein. The > output coordinate files are .dcd. I want to read this file by > fortran code. Is it possible? If so how I will do that. If anybody > gives any sample code for reading reading that specific file. It will > very helpful to me. > > Thanks and regards > Sudipta From owner-chemistry@ccl.net Wed Jun 11 12:56:00 2008 From: "Joseph M Leonard jleonard42]*[gmail.com" To: CCL Subject: CCL: Looking for aligned steroid dataset Message-Id: <-37138-080611120728-6994-VNC8NBRcYCNG1/5h8oTS9w]=[server.ccl.net> X-Original-From: "Joseph M Leonard" Content-Type: multipart/alternative; boundary="----=_Part_15207_28094198.1213198681402" Date: Wed, 11 Jun 2008 11:38:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Joseph M Leonard" [jleonard42#%#gmail.com] ------=_Part_15207_28094198.1213198681402 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, does anybody have an SD file with the aligned "steroid dataset' mentioned in the original CoMFA paper (JACS 110, 5959(1988) or mentioned/realigned in Jewell et al's J Mol Graph Model 20,111(2001) paper (particularly the data leading to Figure 6)? I do not seem to find any supplimentary information associated with either article on-line. Pointers welcome! Thanks in advance! Joe Leonard jleonard42_+_gmail.com -- The most amazing achievement of the computer software industry is its continuing cancellation of the steady and staggering gains made by the computer hardware industry. ------=_Part_15207_28094198.1213198681402 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, does anybody have an SD file with the aligned "steroid dataset' mentioned in the original CoMFA paper (JACS 110, 5959(1988) or mentioned/realigned in Jewell et al's J Mol Graph Model 20,111(2001) paper (particularly the data leading to Figure 6)?  I do not seem to find any supplimentary information associated with either article on-line.  Pointers welcome!

Thanks in advance!

Joe Leonard
jleonard42_+_gmail.com

--
The most amazing achievement of the computer software industry is its continuing cancellation of the steady and staggering gains made by the computer hardware industry.
------=_Part_15207_28094198.1213198681402-- From owner-chemistry@ccl.net Wed Jun 11 13:31:00 2008 From: "John McKelvey jmmckel]~[gmail.com" To: CCL Subject: CCL: recommendation for workstation purchase Message-Id: <-37139-080611100226-905-lqcYtQU6pCDssK4bWuJCYQ^^server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_16883_30001157.1213192933826" Date: Wed, 11 Jun 2008 10:02:13 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel:gmail.com] ------=_Part_16883_30001157.1213192933826 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have been using JNCS.com (Fairport, NY) for the past 10 years, from dual Intel P3, AMDXP+1600, Dual Xeons, and dual-dual AMD's, sometime as assembled/tested motherboard/cpu/memory to fully assembled and tested, all based on ASUS or Supermicro mobos. Though the early AMD's are almost 10 years old they are always try to answer questions as long as they can find the purchase order in their system. They have a very broad variety of quality components, and will build to specs. John McKelvey On Tue, Jun 10, 2008 at 10:07 PM, Zsolt Zsoldos zsolt(~)simbiosys.ca < owner-chemistry .. ccl.net> wrote: > > Sent to CCL by: "Zsolt Zsoldos" [zsolt * simbiosys.ca] > Rachelle, > > If you are looking for pre-built complete systems with good quality > parts and full linux compatibility and support, then I recommend you > to look at this company: > http://www.aslab.com/ > > I have been ordering various machines from them for the last 10 years > and they work well, even today we are still running the first dual P3 > system we bought from them in 1998 (although it has been downgraded > > from workstation to web server by now). > > Best regards, > Zsolt Zsoldos > http://www.simbiosys.ca/ > > On Tue, Jun 10, 2008 at 6:13 PM, Kalju Kahn kalju()chem.ucsb.edu > wrote: > > > > Sent to CCL by: "Kalju Kahn" [kalju[a]chem.ucsb.edu] > > Rachelle, > > > > Are you thinking of self-assembly or a prebuilt machine? I have been > > happy with self-built machines around Gigabyte or Abit motherboards based > > on Intel P35 or X38 chipsets stuffed with 6-8 GB of DDR2 memory. > > Processors like E8400 or Q9300 are affordable and sufficient for what you > > describe. > > > > If you are thinking of stereo, Quadro FX1400 (128 MB RAM) performs OK for > > small proteins ... it is old technology but newer stereo-enabled cards > > (Quadro 3500 Quadro 3700) are rather expensive. FX1400 runs nicely on > > CentOS, and supports dual monitors (consider CRT for full-screen > > visualization + LCD for concurrent text work) > > > > Best luck, > > > > Kalju > > > >> > >> Sent to CCL by: "Rachelle Joyce Bienstock" [biensto1(0)niehs.nih.gov] > >> > >> Hi: > >> > >> I am looking to purchase a dual processor workstation to do > >> some homology modeling and run small MD simulations (AMBER,CHARMM, NAMD) > >> and > >> commercial Schrodinger and Accelrys software packages, and to use > >> to set up jobs to be exported to a big cluster, as well as view results > >> for visualization... with a > >> high-end good graphics card, running Linux Centos 5 and I was looking > >> for recommendations on which processors,which vendors and which > >> machines... > >> > >> Thanks, Rachelle> > >> > >> > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dr. Kalju Kahn > > Department of Chemistry and Biochemistry > > UC Santa Barbara, CA 93106> > > ------=_Part_16883_30001157.1213192933826 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have been using JNCS.com (Fairport, NY) for the past 10 years, from dual Intel P3, AMDXP+1600, Dual Xeons, and dual-dual AMD's, sometime as assembled/tested motherboard/cpu/memory to fully assembled and tested, all based on ASUS or Supermicro mobos.  Though the early AMD's are almost 10 years old they are always try to answer questions as long as they can find the purchase order in their system. 

They have a very broad variety of quality components, and will build to specs.

John McKelvey

On Tue, Jun 10, 2008 at 10:07 PM, Zsolt Zsoldos zsolt(~)simbiosys.ca <owner-chemistry .. ccl.net> wrote:

Sent to CCL by: "Zsolt Zsoldos" [zsolt * simbiosys.ca]
Rachelle,

If you are looking for pre-built complete systems with good quality
parts and full linux compatibility and support, then I recommend you
to look at this company:
http://www.aslab.com/

I have been ordering various machines from them for the last 10 years
and they work well, even today we are still running the first dual P3
system we bought from them in 1998 (although it has been downgraded
> from workstation to web server by now).

Best regards,
Zsolt Zsoldos
http://www.simbiosys.ca/

On Tue, Jun 10, 2008 at 6:13 PM, Kalju Kahn kalju()chem.ucsb.edu
<owner-chemistry|ccl.net> wrote:
>
> Sent to CCL by: "Kalju Kahn" [kalju[a]chem.ucsb.edu]
> Rachelle,
>
> Are you thinking of self-assembly or a prebuilt machine?  I have been
> happy with self-built machines around Gigabyte or Abit motherboards based
> on Intel P35 or X38 chipsets stuffed with 6-8 GB of DDR2 memory.
> Processors like E8400 or Q9300 are affordable and sufficient for what you
> describe.
>
> If you are thinking of stereo, Quadro FX1400 (128 MB RAM) performs OK for
> small proteins ... it is old technology but newer stereo-enabled cards
> (Quadro 3500 Quadro 3700) are rather expensive.  FX1400 runs nicely on
> CentOS, and supports dual monitors (consider CRT for full-screen
> visualization + LCD for concurrent text work)
>
> Best luck,
>
> Kalju
>
>>
>> Sent to CCL by: "Rachelle Joyce Bienstock" [biensto1(0)niehs.nih.gov]
>>
>> Hi:
>>
>> I am looking to purchase a dual processor workstation to do
>> some homology modeling and run small MD simulations (AMBER,CHARMM, NAMD)
>> and
>> commercial Schrodinger and Accelrys software packages, and to use
>> to set up jobs to be exported to a big cluster, as well as view results
>> for visualization... with a
>> high-end good graphics card, running Linux Centos 5 and I was looking
>> for recommendations on which processors,which vendors and which
>> machines...
>>
>> Thanks, Rachelle>
>>
>>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Kalju Kahn
> Department of Chemistry and Biochemistry
> UC Santa Barbara, CA 93106>
>
>



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------=_Part_16883_30001157.1213192933826-- From owner-chemistry@ccl.net Wed Jun 11 14:06:00 2008 From: "Ted Cabeen cabeen-*-chem.ucsb.edu" To: CCL Subject: CCL: recommendation for workstation purchase Message-Id: <-37140-080611125633-26439-Niv0ylhlcF9pfGV1oIJ+gQ%server.ccl.net> X-Original-From: Ted Cabeen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 11 Jun 2008 09:06:16 -0700 MIME-Version: 1.0 Sent to CCL by: Ted Cabeen [cabeen#%#chem.ucsb.edu] Kalju Kahn kalju()chem.ucsb.edu wrote: > If you are thinking of stereo, Quadro FX1400 (128 MB RAM) performs OK for > small proteins ... it is old technology but newer stereo-enabled cards > (Quadro 3500 Quadro 3700) are rather expensive. FX1400 runs nicely on > CentOS, and supports dual monitors (consider CRT for full-screen > visualization + LCD for concurrent text work) Another stereo option is the Quadro FX 560. This is a newer card than the FX 1400, which support blue-line stereo. (Thus you will need a StereoEnabler, as it doesn't have a hardware port) Still, the 560 + enabler is a lot cheaper than the 3700s. Note that the 570 and newer models do not support blue-line stereo. --Ted From owner-chemistry@ccl.net Wed Jun 11 16:20:00 2008 From: "Alex Naden anaden() fsmail.net" To: CCL Subject: CCL: Morphy98 Message-Id: <-37141-080611161224-32430-mDvFBOEXVmT5zj6uaZrJJg:_:server.ccl.net> X-Original-From: "Alex Naden" Date: Wed, 11 Jun 2008 16:12:20 -0400 Sent to CCL by: "Alex Naden" [anaden(a)fsmail.net] Hi, Just to let everyone who answered (on and off the site) that the program finally worked!!!!!!!!! There was a problem with the Gamess .wfn file format. At the moment I just change them manually (with small files), because I am still finding out about the 'reformatting script' writing, but it works! Thanks to everyone for help. I am not sure if anyone (CCL space) will know the answer to this question but any help will be much appreciated. A question: I am trying to set DSL Linux (2.4.81 version) to integrate with Windows, so I can transfer files between the two. The option I get in Linux is SMBCLIENT command (FTP-like access to Windows), which asks me about Domain, Machine, Share etc. Where do I get this information and is there any other option to link the two? Thank you, Alex From owner-chemistry@ccl.net Wed Jun 11 23:04:01 2008 From: "David Emole ikemole]~[yahoo.com" To: CCL Subject: CCL: How to model nanoparticles using Materials Studio Message-Id: <-37142-080611112617-3033-2+WsUYZZ4c8Rr15RLdwfCw%%server.ccl.net> X-Original-From: "David Emole" Date: Wed, 11 Jun 2008 11:26:13 -0400 Sent to CCL by: "David Emole" [ikemole|,|yahoo.com] Does anyone know how to model nanoparticles in Materials Visualizer (Materials Studio). I am working on a project to embed nanoparticles in conjugated polymers using Materials Studio and i have difficulty in modelling the nanoparticles. Please, if you know how to do that, you could help me with that.