From owner-chemistry@ccl.net Sat Mar 25 05:07:00 2006 From: "Eike Huebner eike.huebner:uni-konstanz.de" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31324-060324183355-3495-QWshsrSqODUT2u0qOBmVnw]=[server.ccl.net> X-Original-From: "Eike Huebner" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 25 Mar 2006 00:33:13 +0100 Mime-Version: 1.0 Sent to CCL by: "Eike Huebner" [eike.huebner=uni-konstanz.de] >> Anyway, I want to build a small linux cluster [6-8 total processors] but >> don't have a lot of cooling in one place. Running wires would not be >> practical, if not impossible Now, the application is extremely >> coarse-grain, and only a very, very small amount of data gets moved >> about once initialization of a job is done.. Can it be done "wireless?" >> I know this is not a real answer to this question, but since you are just looking for about 6-8 cpus - why not choose just one board with 2 or four dual-core cpus? It can really fit into just one desktop case and cooling is not really a problem (depending on your other hardware, I wouldn't put 8 disks in there) in normal tower-cases (instead in 19" racks, then its a problem) and maybe you could be more happy with 4-8 cpu's running at slightly lower speed (cool) instead heaving wireless LAN. We are running dual-cpu machines in usual tower cases in rooms without any air-conditioning stable. From owner-chemistry@ccl.net Sat Mar 25 08:41:01 2006 From: "jrui()ci.uc.pt" To: CCL Subject: CCL: how to make psfgen input for estrogen receptor Message-Id: <-31325-060324212433-2694-soKY9vKel0mcYy0+6Wh7Hw=server.ccl.net> X-Original-From: jrui[a]ci.uc.pt Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Sat, 25 Mar 2006 01:22:57 +0000 MIME-Version: 1.0 Sent to CCL by: jrui-,-ci.uc.pt Hi, Your protein contains more than one chain. You should prepare separate PDB files for each chain (A, B, C, D). See http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf Hope this helps, Rui Rodrigues Quoting "s204ira-,-mail.chem.itb.ac.id" : > Sent to CCL by: s204ira:-:mail.chem.itb.ac.id > > I am trying to dock estrogen receptor (1x7j.pdb) with isoflavon. Before > docking, i want to minimize the energy of estrogen receptor with NAMD. > When I try to minimize the energy with NAMD, I have problem with psfgen > input. The input is : > > topology top_all27_prot_lipid.inp > pdbalias residue HIS HSE > segment prot { > pdb 1x7j_prot.pdb > first NTER > last CTER > } > pdbalias atom ILE CD1 CD > coordpdb 1x7j_prot.pdb prot > pdbalias residue HOH TIP3 > segment wat { > pdb 1x7j_solv.pdb > auto none > first none > last none > } > pdbalias atom TIP3 O OH2 > coordpdb 1x7j_solv.pdb wat > guesscoord > writepsf 1x7jnew.psf > writepdb 1x7jnew.pdb > > error message that i receive is: > > error duplicate residue 263 > .. > error duplicate residue 436 > > I found no solution to this problem. > could anyone help me to solve this problem?! > I really appreciate for your help. > > --ira> > > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Sat Mar 25 09:15:00 2006 From: "Steve Bowlus chezbowlus_._goldrush.com" To: CCL Subject: CCL: how to choose the bioactive conformation for CoMFA? Message-Id: <-31326-060324235755-4093-K2SIUHMYfUainovWkMegDg*server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 20:57:28 -0800 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus:-:goldrush.com] $0.02: Remember for a CoMFA model that _change_ in the steric and electrostatic fields is correlated with _change_ in biological endpoint. We are modeling _variance_ not some absolute property. For reasonably congeneric series, an energetically reasonable conformation will yield a workable model, provided that changes in different parts of a molecule can be assumed to be independent of one another. As a thought experiment, consider aromatic substitution on a phenethyl moiety: changes in substitution in the m and p positions will have little effect on the conformation of the chain, while o (and/or o') substitution may affect the chain-ring dihedral only. An alignment with an extended, transoid ethyl chain will give a workable model, even if this is not the global energy minimum, much less the bioactive conformation. This type of model will break down (rapidly!) when other, non-congeneric molecules are added to the data set. These new molecules effectively add new constraints to the system and a new alignment rule incorporating the constraints must be developed. It is certainly desirable to model something approaching the bioactive conformation, since all active molecules (congeneric or not) will necessarily satisfy the physical constraints of the binding site, but this is not a requirement for a successful CoMFA model. Steve Dominic Ryan dominic.ryan,,comcast.net wrote: > Sent to CCL by: "Dominic Ryan" [dominic.ryan _ comcast.net] > It is important to realize that there are usually a reasonably large number > of low energy conformations and that picking the lowest is no assurance that > you have picked the relevant one. > > In addition, one has to worry about lowest *free* energy, and in the right > environment, not simple mechanics minimization. > > Dominic Ryan > > -----Original Message----- > >>From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] > > Sent: Friday, March 24, 2006 5:55 PM > To: Ryan, M Dominic > Subject: CCL: how to choose the bioactive conformation for CoMFA? > > Sent to CCL by: "Pankaj Daga" [pdaga+*+olemiss.edu] > IN many cases, if the bioactive conformation is not > available, the minimum energy conformation is considered to > be the bioactive conformation. > > Minimum energy conformation can be obtained by > conformational search of the molecule. > > Cheers > > panda > > > > >>Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com] >>C Sakthivel wrote: >> >>>How do I choose the bioactive conformation of a >>>perticular compound if such type of compounds were not >> >>investigated earlier? >> >>I'd be surprised if there were a general method for >>this...it all depends on which proteins it's supposed to >>interact with (the bioactive conformation would be >>whichever conformation fits the protein better), and it >>doesn't sound like you have that information. >> >> >>--David Shobe, Ph.D., M.L.S. >>Süd-Chemie, Inc. >>phone (502) 634-7409 >>fax (502) 634-7724 >> >>Don't bother flaming me: I'm behind a firewall. >> >> >> >> >> >>-----Original Message----- >> >>>From: owner-chemistry()ccl.net >> >>[mailto:owner-chemistry()ccl.net] Sent: Wednesday, March >>22, 2006 6:48 PM To: Shobe, David >>Subject: CCL: how to choose the bioactive conformation for >>CoMFA? >> >>Sent to CCL by: Sakthivel C [skvchem[]yahoo.com] >>--0-882663183-1143036218=:29550 Content-Type: > > text/plain; > >>charset=iso-8859-1 Content-Transfer-Encoding: 8bit >> >>Dear CCLers, >> I'm working on 3D QSAR studies of some ancancer drugs >>that are developed in our lab. Former members of our >>group synthesized & studied the ancancer activity for >>those compounds. I want to use the activity data for my >>3D QSAR studies (CoMFA & CoMSIA) and identify some new >>compounds in same series. I learnt that choosing a wrong >>bioactive conformer would lead to worng results. >> So, my question is >> How do I choose the bioactive conformation of a >>perticular compound if such type of compounds were not >>investigated earlier? >> >> Can any one suggest me? >> >> Looking forward to hear from you. >> >> Sincerely, >> >> C Sakthivel >> Bharathidasan University >> India >> >> >>C. SAKTHIVEL >>Research Scholar >>School of Chemistry >>Bharathidsan University >>Tiruchirappalli 620 024 >>TN, India >>E-mail: skvchem~!~yahoo.com >> skv_chem~!~yahoo.co.in >> >> >> >> >>--------------------------------- >> Yahoo! Mail >> Use Photomail to share photos without annoying >>attachments. --0-882663183-1143036218=:29550 >>Content-Type: text/html; charset=iso-8859-1 >>Content-Transfer-Encoding: 8bit >> >>
Dear CCLers,
I'm working on 3D QSAR >>studies of some ancancer drugs that are developed in our >>lab. Former members of our group synthesized & >>studied the ancancer activity for those compounds. I >>want to use the activity data for my 3D QSAR studies >>(CoMFA & CoMSIA) and identify some new compounds >>in same series. I learnt that choosing a wrong >>bioactive conformer would lead to worng results. >>
So, my question is
How >>do I choose the bioactive conformation of a perticular >>compound if such type of compounds were not >>investigated earlier?
>>
Can any one suggest me?
>>
Looking forward to hear from you.
>>;
Sincerely,
C >>Sakthivel
Bharathidasan University
>>
India

> >
>
>>color=#00007f>C. SAKTHIVEL> FONT>
> color=#ff007f>Research > >>Scholar
>color=#ff007f>School of Chemistry
> >
>>face=arial color=#ff007f>Bharathidsan >>University
>color=#ff007f>Tiruchirappalli 620 024
>>
TN, > > India
> >> >>

>>

Yahoo! Mail
>>> > > href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=3886 > >>7/*http://photomail.mail.yahoo.com">Use Photomail to >>share photos without annoying attachments. >> > > --0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bi > >>n/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_uns >>ub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message >>may contain confidential and / or privileged information. >>If you are not an addressee or otherwise authorized to >>receive this message, you should not use, copy, disclose >>or take any action based on this e-mail or any information >>contained in the message. If you have received this >>material in error, please advise the sender immediately by >>reply e-mail and delete this message. Thank you. >> >> >> >>-= This is automatically added to each message by the >>mailing script =- To recover the email address of the >>author of the message, please change the strange >>characters on the top line to the _._ sign. You can also> Conferences: >>http://server.ccl.net/chemistry/announcements/conferences/ >> >>Search Messages: http://www.ccl.net/htdig (login: ccl, >>Password: search)> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >>-+-+-+-+-+-+-+ >> >> >> >> > > > Pankaj R. Daga > Department of Medicinal Chemistry > School of Pharmacy > 417 Faser Hall > University of Mississippi > University, MS, 38677-1848 > USAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > > From owner-chemistry@ccl.net Sat Mar 25 15:56:00 2006 From: "Xiaowei (David) Li xl3a(!)virginia.edu" To: CCL Subject: CCL: GAMESS for DNA Message-Id: <-31327-060324175228-10035-NXACPGNVAmxstGhXBYAG3w|a|server.ccl.net> X-Original-From: "Xiaowei (David) Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 16:58:07 -0500 MIME-Version: 1.0 Sent to CCL by: "Xiaowei (David) Li" [xl3a]=[virginia.edu] Dear CCLers: I am current working on the investiation of DNA vibrational modes. I know it is generally NOT possible to calcualte normal modes of DNA with hundreds of base pairs using GAMESS, even for parallized one. However, I am wondering whether it is possible to do ab initio calculation of DNA with 10 base pairs (around 700 atoms) using parallized GAMESS within reasonable time period. Thank you in advance. Best. Xiaowei Li University of Viriginia From owner-chemistry@ccl.net Sat Mar 25 16:31:00 2006 From: "Mehmed Zahid ERTEM mzertem*|*gmail.com" To: CCL Subject: CCL:G: Inv2 error Message-Id: <-31328-060325093638-16185-tlvfyTwp/KULOfHT0EValw],[server.ccl.net> X-Original-From: "Mehmed Zahid ERTEM" Date: Sat, 25 Mar 2006 09:36:37 -0500 Sent to CCL by: "Mehmed Zahid ERTEM" [mzertem_-_gmail.com] Hi to all, I am trying to perform a solvent optimization process with my molecule via G03 with the following method: B3LYP/6-31+G** opt=gdiis freq scrf=(iefpcm,solvent=water,read) .. .. .. bondi=radii and my job terminates (after many cycles and steps) with the following message: "Inv2 failed in DMIVCL" I want to learn the meaning of the error message and how I could overcome this problem, thank you all, good luck with your computations From owner-chemistry@ccl.net Sat Mar 25 17:24:00 2006 From: "Caio Julio Martins Veloso cveloso]-[pucminas.br" To: CCL Subject: CCL: Benzamidine parameters Message-Id: <-31329-060325143947-6530-A1V0LDS90VlU5goCAQdmbg^server.ccl.net> X-Original-From: "Caio Julio Martins Veloso" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 25 Mar 2006 15:57:38 -0300 MIME-Version: 1.0 Sent to CCL by: "Caio Julio Martins Veloso" [cveloso a pucminas.br] Hi all, Does anyone have CHARMM force field parameters for benzamidine (C7H8N2)? Thanks, Caio.