From jkl@ccl.net Tue Jan 13 07:21:19 2004 -0500 Return-Path: Date: Tue, 13 Jan 2004 13:20:32 +0100 Message-ID: <4002B18800001981^at^ims1b.cp.tin.it> From: sa.cosco^at^virgilio.it Subject: MD after Autodock To: chemistry^at^ccl.net Dear CCL I performed a partial flexible docking analysis of some ligands, using Autodock, on a receptor modelled by means of homology building .The complexes obtained were geometrically optimized and energetically minimized. Is it really necessary to perform a MD simulation after the docking and the minimization? Any suggestion will be appreciated Best regards Sandro From chemistry-request@ccl.net Mon Jan 12 21:39:31 2004 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0D2dUld030638 for ; Mon, 12 Jan 2004 21:39:30 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.10/8.12.10/GSC1.16) with ESMTP id i0D2e5hH793955 for ; Mon, 12 Jan 2004 18:40:05 -0800 (PST) Date: Mon, 12 Jan 2004 18:40:05 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry-.at.-ccl.net Subject: heat capacity of supercooled water!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I am looking for estimation of heat capacity at constant volume (Cv) of supercooled water from simulation. I got references only at constant pressure. Any pointer would be appreciated. Also, any pointer to the experimental Cv for supercooled water will be very helpful to me. thanks. Pradipta From chemistry-request@ccl.net Tue Jan 13 12:28:16 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0DHSAld008634 for ; Tue, 13 Jan 2004 12:28:14 -0500 Received: from smeagol.unb.ca (smeagol.unb.ca [131.202.3.52]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id i0DHRuDa014407; Tue, 13 Jan 2004 13:28:06 -0400 Received: from smeagol.unb.ca (localhost.localdomain [127.0.0.1]) by smeagol.unb.ca (8.12.8/8.12.8) with ESMTP id i0DHRehT020564; Tue, 13 Jan 2004 13:27:40 -0400 Received: (from apache@localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id i0DHRdpg020561; Tue, 13 Jan 2004 13:27:39 -0400 Received: from athlon2.chem.unb.ca (athlon2.chem.unb.ca [131.202.171.176]) by webmail.unb.ca (IMP) with HTTP for ; Tue, 13 Jan 2004 13:27:39 -0400 Message-ID: <1074014859.40042a8b99d35.-at-.webmail.unb.ca> Date: Tue, 13 Jan 2004 13:27:39 -0400 From: Joey Harriman To: sa.cosco.-at-.virgilio.it Cc: chemistry.-at-.ccl.net Subject: Re: CCL:MD after Autodock References: <4002B18800001981.-at-.ims1b.cp.tin.it> In-Reply-To: <4002B18800001981.-at-.ims1b.cp.tin.it> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.171.176 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-2.4, required 5, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, SPAM_PHRASE_03_05, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Sandro, I'm not really sure what you are trying to do....Did you perform the geometry optimization and minimization to both the ligand and the receptor? In addition, do you mean that you optimized (via ab initio) then minimized (using MM)? If you are trying to find the best docking pose of a ligand to a given receptor here is what I would do: 1. Optimize the active site of the receptor (if you don't have a crystal structure) and the ligand i.e. ab initio geometry optimization. If you do this at the HF/6-31G* level then you can generate a RESP charge set which is excellent for docking. 2. Do the docking in Autodock. 3. Rescore the poses. The scoring function in Autodock is not necessarily the best. It was trained on a limited number of molecules and used OPLS charges. You can however rescore the poses using a MM program that will allow you to calculate VdW, electrostatic, potential energy (of ligand), etc...and use this to rank the poses. As far as a MD simulation.....you could do one if you wanted to observe the interaction between the ligand and the receptor. This might be useful to determine if the ligand is equilibrated (i.e. prefers one geometry) in the active site and the rate at which it goes into and out of the active site. Hope this helps. Cheers, Joey ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o.-at-.unb.ca 476-6543 ---------------------------------- Quoting sa.cosco.-at-.virgilio.it: > Dear CCL > I performed a partial flexible docking analysis of some ligands, using Autodock, > on a receptor modelled by means of homology building .The complexes obtained > were geometrically optimized and energetically minimized. Is it really necessary > to perform a MD simulation after the docking and the minimization? Any suggestion > will be appreciated > Best regards > Sandro > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY.-at-.ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow.-at-.nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Jan 13 08:04:46 2004 Received: from avmx.iitkgp.ernet.in ([203.197.98.4]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0DD4gld025725 for ; Tue, 13 Jan 2004 08:04:44 -0500 Received: from avmx.iitkgp.ernet.in (avmx [203.197.98.4]) by avmx.iitkgp.ernet.in (8.12.5/8.12.5) with ESMTP id i0DDbNgF001516 for ; Tue, 13 Jan 2004 19:07:23 +0530 Received: from iitkgp.iitkgp.ernet.in (iitkgp.iitkgp.ernet.in [203.197.98.10]) by avmx.iitkgp.ernet.in (8.12.5/8.12.5) with ESMTP id i0DDbNbb001511 for ; Tue, 13 Jan 2004 19:07:23 +0530 Received: from cts.iitkgp.ernet.in (localhost [127.0.0.1]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id SAA23829 for ; Tue, 13 Jan 2004 18:25:40 -0500 (GMT) X-Authentication-Warning: iitkgp.iitkgp.ernet.in: iscan owned process doing -bs Received: from localhost (utpal@localhost) by cts.iitkgp.ernet.in (8.11.6/8.11.6) with ESMTP id i0DCb2523914 for ; Tue, 13 Jan 2004 18:07:11 +0530 Date: Tue, 13 Jan 2004 18:07:02 +0530 (IST) From: utpal sarkar To: chemistry[at]ccl.net Subject: Stochastic Resonance Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL Users, I am trying to calculate Signal to noise ratio for a stochastic system (with white noise). I can't understand how to calculate the noise power and signal power? Is there any free fortran/C progam available for this? Any kind of help is greatly acknowledged. Thanking you. With regards Utpal Sarkar Indian Institute Of Technology Kharagpur-721302 INDIA From chemistry-request@ccl.net Tue Jan 13 14:28:49 2004 Received: from hubble.deepsea.com (ip67-89-181-114.z181-89-67.customer.algx.net [67.89.181.114]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0DJSbld013582 for ; Tue, 13 Jan 2004 14:28:44 -0500 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: RE: Stochastic Resonance Date: Tue, 13 Jan 2004 11:29:09 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Stochastic Resonance Thread-Index: AcPaCIJMowLdwiqZQE27GsXdHULoEwAAYhEQ From: "Ray Merewether" To: "utpal sarkar" , X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by servernd.ccl.net id i0DJSnld013591 If your system is really white and passive, kTB should be a very good approximation to the noise power and a slide rule will suffice ( like Penzias and Wilson 1965). If you have active semiconductors, like a Zener at breakdown, the noise power may be an order of magnitude higher. To say anything about signal, one needs to know a lot more about the system. Berkeley SPICE in its various incarnations can calculate SNR for lumped equivalent systems. I have used it to calculate plane wave acoustic noise amplitudes and velocities in solids and fluids. You just need to map the mechanical masses, stiffnesses, etc. over to electrical properties in a reasonable manner. -----Original Message----- From: utpal sarkar [mailto:utpal-.at.-cts.iitkgp.ernet.in] Sent: Tuesday, January 13, 2004 4:37 AM To: chemistry-.at.-ccl.net Subject: CCL:Stochastic Resonance Dear CCL Users, I am trying to calculate Signal to noise ratio for a stochastic system (with white noise). I can't understand how to calculate the noise power and signal power? Is there any free fortran/C progam available for this? Any kind of help is greatly acknowledged. Thanking you. With regards Utpal Sarkar Indian Institute Of Technology Kharagpur-721302 INDIA -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY-.at.-ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Jan 13 15:24:17 2004 Received: from cornell.edu (cornell.edu [132.236.56.6]) by servernd.ccl.net (8.12.8/8.12.8) with ESMTP id i0DKODld014767 for ; Tue, 13 Jan 2004 15:24:13 -0500 Received: from cornell.edu (kili.ccmr.cornell.edu [128.84.241.146]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id PAA02800 for ; Tue, 13 Jan 2004 15:24:50 -0500 (EST) Message-ID: <40045412.3080608[at]cornell.edu> Date: Tue, 13 Jan 2004 15:24:50 -0500 From: Connie Chang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030703 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: CCL:G98 & LINDA question Content-Type: multipart/alternative; boundary="------------000900070505040506060007" X-Spam-Status: No, hits=1.4 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_MESSAGE, HTML_TITLE_EMPTY autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------000900070505040506060007 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi I also have a question regarding a parallel job I am running on an already optimized geometry. I am trying to get the frequencies/modes with the following simple route: %mem=10000000 %NProcLinda=3 %rwf=/scratch/cc236/G98Batch/tempor1.rwf,200MW,/scratch/cc236/G98Batch/tempor2.r wf,200MW,/scratch/cc236/G98Batch/tempor3.rwf,200MW,/scratch/cc236/G98Batch/tempo r4.rwf,200MW,/scratch/cc236/G98Batch/tempor5.rwf,-1 %chk=c72dftparallel.chk #B3LYP 6-31G SCF=(MaxCyc=2000) Geom=Allcheck Guess=Read Freq Test This is what I am getting in output so far that concerns me. The job has ran so far for about 20 hours... A short cut and paste section follows the brief descriptions below (output is in bold): What do the warnings mean where it says that the *smallest alpha delta epsilon is 0.57239995D-01* and the *largest alpha MO coefficient is 0.17407377D+02*? And what does this line mean: *PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda.* Does it mean that instead of running a parallel job it is running serial now for some reason? *Requested convergence on RMS density matrix=1.00D-08 within2000 cycles. Requested convergence on MAX density matrix=1.00D-06. SCF Done: E(RB+HF-LYP) = -2741.84228534 A.U. after 2 cycles Convg = 0.6529D-08 -V/T = 2.0051 S**2 = 0.0000 Range of M.O.s used for correlation: 1 648 NBasis= 648 NAE= 216 NBE= 216 NFC= 0 NFV= 0 NROrb= 648 NOA= 216 NOB= 216 NVA= 432 NVB= 432 **** Warning!!: The largest alpha MO coefficient is 0.17407377D+02 **** Warning!!: The smallest alpha delta epsilon is 0.57239995D-01 PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. G2DrvN: will do 2 atoms at a time, making 36 passes doing MaxLOS=1. * Thanks, Connie --------------000900070505040506060007 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi

I also have a question regarding a parallel job I am running on an already optimized geometry.  I am trying to get the frequencies/modes with the following simple route:
 
%mem=10000000
 %NProcLinda=3
 %rwf=/scratch/cc236/G98Batch/tempor1.rwf,200MW,/scratch/cc236/G98Batch/tempor2.r
 wf,200MW,/scratch/cc236/G98Batch/tempor3.rwf,200MW,/scratch/cc236/G98Batch/tempo
 r4.rwf,200MW,/scratch/cc236/G98Batch/tempor5.rwf,-1
 %chk=c72dftparallel.chk
 
 #B3LYP 6-31G SCF=(MaxCyc=2000) Geom=Allcheck Guess=Read Freq Test

This is what I am getting in output so far that concerns me.  The job has ran so far for about 20 hours...  A short cut and paste section follows the brief descriptions below (output is in bold):

What do the warnings mean where it says that the smallest alpha delta epsilon is  0.57239995D-01 and the largest alpha MO coefficient is  0.17407377D+02?

And what does this line mean:  PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.

Does it mean that instead of running a parallel job it is running serial now for some reason?


Requested convergence on RMS density matrix=1.00D-08 within2000 cycles.
Requested convergence on MAX density matrix=1.00D-06.
SCF Done:  E(RB+HF-LYP) =  -2741.84228534     A.U. after    2 cycles
            Convg  =    0.6529D-08             -V/T =  2.0051
            S**2   =   0.0000
Range of M.O.s used for correlation:     1   648
NBasis=   648 NAE=   216 NBE=   216 NFC=     0 NFV=     0
NROrb=    648 NOA=   216 NOB=   216 NVA=   432 NVB=   432

**** Warning!!: The largest alpha MO coefficient is  0.17407377D+02


**** Warning!!: The smallest alpha delta epsilon is  0.57239995D-01

PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda.
G2DrvN: will do    2 atoms at a time, making   36 passes doing MaxLOS=1.


Thanks,
Connie
--------------000900070505040506060007-- From chemistry-request@ccl.net Fri Jan 9 01:04:02 2004 Return-Path: Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0963UX9023803 for ; Fri, 9 Jan 2004 01:03:31 -0500 Received: from yangtze.hku.hk (yangtze.hku.hk [127.0.0.1]) by yangtze.hku.hk (8.12.8/8.12.8) with ESMTP id i0962WXC018047 for ; Fri, 9 Jan 2004 14:02:32 +0800 Received: from localhost (martin@localhost) by yangtze.hku.hk (8.12.8/8.12.8/Submit) with ESMTP id i0962W4M018043 for ; Fri, 9 Jan 2004 14:02:32 +0800 Date: Fri, 9 Jan 2004 14:02:32 +0800 (HKT) From: martin.-at-.yangtze.hku.hk To: chemistry.-at-.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear sir, I wouls like to perform MD simulation of alkanthiol on gold surface with CHARMM. However, there is no parameter for interaction between Au and S, etc. Where can I look for the parameters? Thank you very much yours, Martin