From chemistry-request@ccl.net Wed Jul 30 08:53:53 2003 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UCrq47001143 for ; Wed, 30 Jul 2003 08:53:53 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.20) id 19hqSk-0007ek-Iv; Wed, 30 Jul 2003 14:53:50 +0200 Message-ID: <3F27BFD3.9010709$at$mpi-bpc.mpg.de> Date: Wed, 30 Jul 2003 14:53:39 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: VMD , CCL , namd$at$ks.uiuc.edu Subject: NAMD failure on Berendsen pressure scheme Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Report: -0.5/6.0 ---- Start SpamAssassin results -0.50 points, 6 required; * -0.5 -- User-Agent header indicates a non-spam MUA (Mozilla) ---- End of SpamAssassin results X-Spam-Level: / X-Virus-Scanned: (clean) by exiscan+sophie Dear fellows, If you have some experience with namd could somebody explain why this is happening (see error message at the bottom of the message)? I am using the following script:. It is a constant pressure equilibration using Berendsen algorithm for temp and pressure. This equilibration step follows after a minim and a const Vol. eq in which the temperature is adjusted to 300 (also with temp coupling scheme). The protocol below works fine in AMBER but maybe there some differences between the values used by the 2 programs that I didnt figure out. The first eq. at const Vol works fine both in Amber and Namd so I guess there is something about pressure here. If you want more details please let me know!. I would appreciate any advice. Thank you very much , Vlad # *** AMBER force field *** --------------------------------- amber on parmfile rnaWI.top coordinates rnaWI_mdeq2.pdb.coor readexclusions yes exclude scaled1-4 1-4scaling 0.83333333 #=1/1.2 scnb 2 #*** approximations for nonbonded interactions ------------ switching off cutoff 9 stepspercycle 1 #***equilibration parameters minimization off numsteps 10000 timestep 1.0 #***SHAKE use rigidbonds all #***temperature regulation for equilibration step (NPT) using #***temperature coupling temperature 100.0 tcouple on tcoupletemp 300.0 tcouplefile rnaWI_ceq2.pdb ### friction coef.=1.0 tcouplecol B #***constant pressure equilibration using Berendsen bath coupling usegrouppressure on useflexiblecell on berendsenpressure on berendsenpressuretarget 1.0 berendsenpressurecompressibility 0.0000446 berendsenpressurerelaxationtime 500 berendsenpressurefreq 100 #***PME PME on cellBasisVector1 56.21 0 0 cellBasisVector2 0 58.53 0 cellBasisVector3 0 0 57.89 cellOrigin 0 0 0 PMEGridSizeX 50 PMEGridSizeY 55 PMEGridSizeZ 50 XSTfile rnaWI_mdeq3.XST XSTfreq 200 #***constraints (holding the solute fixed) constraints on consexp 2 consref rnaWI_mdeq2.pdb.coor conskfile rnaWI_res500.pdb conskcol B #***outputnames outputname rnaWI_mdeq3.pdb restartname rnaWI_mdeq3.rst dcdfile rnaWI_mdeq3.dcd dcdfreq 200 veldcdfile rnaWI_mdeq3.vel.dcd veldcdfreq 200 restartfreq 200 outputenergies 100 outputpressure 100 binaryoutput off binaryrestart off ###---error----------------- RESSURE: 300 76798.7 -40631.2 58693.1 -13378.6 29200.3 -5152.76 69223.5 -42523.7 81493.1 GPRESSURE: 300 76687.2 -40836.2 58854.3 -13914.7 29538.5 -4262.26 68552.2 -42832.5 81484.6 ENERGY: 300 2002.7469 2400.4670 550.4454 0.0000 -61779.2755 9089.4231 60866.5902 0.0000 31247.2457 44377.6430 1056.1747 62497.3627 62570.0965 185386.7344 -1757.5130 -1600.7691 ERROR: Constraint failure in RATTLE algorithm for atom 121! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ========================================== -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru$at$mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Wed Jul 30 07:14:22 2003 Received: from bmbpcu21.leeds.ac.uk (bmbpcu21.leeds.ac.uk [129.11.110.201]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UBEL47031447 for ; Wed, 30 Jul 2003 07:14:21 -0400 Received: from peter by bmbpcu21.leeds.ac.uk with local (Exim 3.22 #1) id 19hppF-0008NE-00 for chemistry$at$ccl.net; Wed, 30 Jul 2003 12:13:01 +0000 Content-Type: text/plain; charset="iso-8859-15" From: Peter Oledzki Reply-To: peter$at$bioinformatics.leeds.ac.uk To: chemistry$at$ccl.net Subject: Standard Bond Lengths? Date: Wed, 30 Jul 2003 12:13:01 +0000 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <03073012130100.31948@bmbpcu21> Content-Transfer-Encoding: 8bit Sender: Peter Oledzki Hello CCLers, I'm looking for standard bond lengths between various atoms in organic molecules. I'm using these bond lengths in a molecular mechanics force field (GRID) for flexible ligand docking. I require bond lengths between each atom type i.e. an aromatic carbon and an sp3 NH group with a lone pair etc etc Does anybody know of any resources avialable ? Like a database or websites? Any help on this matter would be greatly appreciated Cheers Peter -- *********************************************************** Peter Oledzki PhD Bioinformatics Research Student School of Biochemistry and Molecular Biology University of Leeds LS2 9JT 0113 3432988 From chemistry-request@ccl.net Tue Jul 29 11:51:22 2003 Received: from iris.chimfarm.unipg.it (iris.chimfarm.unipg.it [141.250.13.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6TFpL47006455 for ; Tue, 29 Jul 2003 11:51:22 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] helo=apollo) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 19hfBI-0004Lj-00 for chemistry$at$ccl.net; Tue, 29 Jul 2003 17:51:04 -0700 From: "Daniele Bellocchi" To: Subject: Summary of ONIOM calculation Date: Tue, 29 Jul 2003 17:50:45 +0200 Message-ID: <000001c355e9$2c4e8470$480dfa8d@apollo> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C355F9.EFD9C570" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C355F9.EFD9C570 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Everyone, I would like to thank who get me the following usefull answer to my question. Original Query: ************** Dear All, i performed a two layers ONIOM calculation (AM1:amber) on a complex enzyme-substrate. The problem that i have is that AMBER requires all the parameters for the ligand, even though the ligand belongs to the QM shell. Is there any ways to circonvent this problem? Thanks in advance. ************** Replies: --------------------------------------------------- Dear Daniele, I have never used AMBER, so maybe what I am going to say is nonsense, but when running QM/MM simulations with CHARMM you also have to provide parameters for the QM part, but as the program does not use them, you can provide any stupid set of numbers as long as they are with the correct format (they are used to create the topology file, but then they are replaced). Maybe you can try this to see if it works. Regards, Olalla Nieto Faza Dpto. Quimica Organica Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain) e-mail: faza$at$uvigo.es ------------------------------------------------------------------------ ------------------------- Mr. Bellocchi, This is a common mis-understanding with the ONIOM method. All atoms are computed at the low level, once with the real system and once with just the model system which are the atoms you have in the QM region. Then a calculation is done with the QM method on the model system and the energy is computed, E(oniom) = E (1) + E (2) - E (2) lo hi lo where 1 is the full set of atoms and 2 are the atoms in the model system. hi and lo refer to the levels of theory. So, you do need to have AMBER parameters for the ligand. In some cases the contributions will cancel but not always and so Gaussian computes them. Which version of Gaussian are you using? Gaussian 03 allows you to supply additional parameters which can fix most of these cases. Douglas J. Fox Technical Support Gaussian, Inc. help$at$gaussian.com ----------------------------------------------------------------- Hello Daniele, As far as I am aware, the reason why potentials for the entire system would be required is because of the way ONIOM uses to calculate the energies (of the QM part of your system). Briefly E (whole) = E (AM1,QM part) + E (AMBER, whole) - E (AMBER, QM part) A better explanation can be found in: I. Roggero, B. Civalleri, P. Ugliengo, Chem. Phys. Letts. 341 (2001) 625-632 Plus also the original Morokuma papers about ONIOM. Hope this helps to some extent. Good luck Best Regards Naseem Naseem A. Ramsahye Postdoctoral Researcher Royal Institution of Great Britain 21 Albemarle Street, London, W1S 4BS, UK Website: www.ri.ac.uk/DFRL/N.Ramsahye ------------------------------------------------------------------------ - Best Regards Daniele Bellocchi, PhD Student Molecular Modeling Section Istituto di Chimica e Tecnologia del Farmaco University of Perugia Italy ------=_NextPart_000_0001_01C355F9.EFD9C570 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Everyone,

I would like to thank who get me the following usefull answer to my = question.

 

Original Query:

**************

 

Dear All,

i performed a two layers ONIOM calculation (AM1:amber) on a complex enzyme-substrate. The problem that i have is that AMBER requires all the parameters for the ligand, even though the ligand belongs to the QM = shell.

Is there any ways to circonvent this problem?

Thanks in advance.

 

**************

 

 

Replies:

-------------------------------------------= --------

Dear = Daniele,

I have never used AMBER, so maybe = what I am going to say is nonsense, but when running QM/MM simulations with = CHARMM you also have to provide parameters for the QM part, but as the program does = not use them, you can provide any stupid set of numbers as long as they are = with the correct format (they are used to create the topology file, but then = they are replaced). Maybe you can try this to see if it works. = Regards,

 

 

Olalla Nieto Faza

Dpto. Quimica Organica

Universidade de Vigo

Lagoas-Marcosende 36200 Vigo (Spain)

e-mail: faza$at$uvigo.es

 

------------------------------------------------------= -------------------------------------------

Mr. = Bellocchi,

 

   This is a common = mis-understanding with the ONIOM method. All atoms are computed at the low level, once = with the real system and once with just the model system which are the atoms you = have in the QM region.  Then a = calculation is done with the QM method on the model system and the energy is = computed,

 

  E(oniom) =3D E (1) + E (2) - E = (2)

       &nbs= p;      lo      hi      = lo

 

where 1 is the full set of atoms = and 2 are the atoms in the model system.  hi and lo refer to the levels of theory.

 

   So, you do need to have = AMBER parameters for the ligand.  = In some cases the contributions will cancel but not always and so Gaussian = computes them.

 

   Which version of Gaussian = are you using?  Gaussian 03 allows = you to supply additional parameters which can fix most of these = cases.

 

Douglas J. Fox

  Technical Support

  Gaussian, Inc.

  help$at$gaussian.com=

 

-----------------------------------------------------------------

Hello = Daniele,

 

As far as I am aware, the reason = why potentials for

the entire system would be = required is because of the

way ONIOM uses to calculate the = energies (of the QM

part of your = system).

 

Briefly

 

E (whole) =3D   E (AM1,QM part) + E = (AMBER, whole)

       &nbs= p;          - E (AMBER, QM part)

 

A better explanation can be found = in:

I. Roggero, B. Civalleri, P. Ugliengo, Chem. Phys.

Letts. 341 (2001) = 625-632

 

Plus also the original Morokuma = papers about ONIOM.

 

Hope this helps to some = extent.

Good = luck

Best = Regards

Naseem

 

Naseem A. = Ramsahye

Postdoctoral = Researcher

Royal Institution of Great = Britain

21 Albemarle Street, London, W1S = 4BS, UK

Website: www.ri.ac.uk/DFRL/N.Ramsahye

 

 

-------------------------------------------= ------------------------------

 

 

Best= Regards

 

Daniele Bellocchi, PhD Student

Molecular Modeling Section

Istituto di Chimica = e Tecnologia del Farmaco

University of Perugia

Italy

 

 

 

------=_NextPart_000_0001_01C355F9.EFD9C570-- From chemistry-request@ccl.net Tue Jul 29 12:34:12 2003 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 h6TGYA47007636 for ; Tue, 29 Jul 2003 12:34:11 -0400 Received: from localhost (martin@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h6TGpPF12329 for ; Wed, 30 Jul 2003 00:51:25 +0800 Date: Wed, 30 Jul 2003 00:51:25 +0800 (HKT) From: Ma Chi Chiu To: CHEMISTRY$at$ccl.net Subject: Question on writing Charmm's input file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, My question is how to calculate the force or interaction force with CHARMM and how to write the corresponding input file? Thank you very much yours, Martin From chemistry-request@ccl.net Wed Jul 30 03:24:38 2003 Received: from richardson.uni2.net (richardson.uni2.net [130.227.52.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6U7Oa47025881 for ; Wed, 30 Jul 2003 03:24:37 -0400 Received: from HLUSF26A.lundbeck.com (mail.lundbeck.com [130.227.160.31]) by richardson.uni2.net (8.11.6/8.11.6) with SMTP id h6U7OZb21618 for ; Wed, 30 Jul 2003 09:24:36 +0200 Received: from ([172.16.0.163]) by HLUSF26A.lundbeck.com; Wed, 30 Jul 2003 09:24:19 +0200 (CEST) Received: FROM ludk0006.lundbeck.com BY ludk0163.lundbeck.com ; Wed Jul 30 09:24:09 2003 +0200 Received: by ludk0006.lundbeck.com with Internet Mail Service (5.5.2653.19) id ; Wed, 30 Jul 2003 09:24:09 +0200 Message-ID: From: Jan Torleif Pedersen To: chemistry$at$ccl.net Subject: Compiling a virtual structural library of metabolic intermediates and natural ligands Date: Wed, 30 Jul 2003 09:24:08 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Greetings, I am in the process of compiling a database of metabolic intermediates (small molecules) and natural ligands. I am aware that this is not a trivial undertaking. - I am planning to make this available on the internet as an interactive database, but I will need a fairly complete startingpoint of annotated 2D/3D structures. I do have a library I have compiled myself already and would like to have user input. Some general questions that someone might like to ponder about are: 1) How large would such a library need to be if we consider both procaryotic and eucaryotic metabolism? 2) How should one deal with tautomers in such a database? Any other suggestions and reflections on the idea are also welcome ! I do NOT need pointers to other databases as you cannot compile databases > from other databases without infringing copyright and ownership - especially if you want to make the data publicly available. Please if you have any sets of ligands/metabolites/catabolites which you feel should be in there I would be happy to add them in. A redundancy check will be performed when adding them to the database. The annotation could contain any of the following fields: Trivial name IUPAC name Structure (sdf) Pathway/Reaction etc ... Many regards -- Jan Dr. Jan Torleif Pedersen Section head, Bioinformatics Department of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 DK-Valby Denmark phone: +45 36 43 28 87 FAX: 36438271 email: jatp$at$lundbeck.com From chemistry-request@ccl.net Wed Jul 30 11:01:52 2003 Received: from mx3.tiki.ne.jp (mx3.tiki.ne.jp [218.40.30.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UF1o47005859 for ; Wed, 30 Jul 2003 11:01:51 -0400 Received: from computer (dadff7-126.tiki.ne.jp [218.223.247.126]) by mx3.tiki.ne.jp (8.9.3p2/3.7W) with SMTP id AAA04008; Thu, 31 Jul 2003 00:01:38 +0900 (JST) Message-ID: <002301c356ae$360fa8c0$7ef7dfda@computer> From: "Masao Masamura" To: "Peter Oledzki" Cc: References: <03073012130100.31948@bmbpcu21> Subject: Re: CCL:Standard Bond Lengths? Date: Thu, 31 Jul 2003 00:21:12 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-15" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear Peter Oledzki, The following article may be useful: J. A. Pople and M. Gordon, J. Am. Chem. Soc. 89, 4253(1967). Best regards, M. Masamura > Hello CCLers, > > I'm looking for standard bond lengths between various atoms in organic > molecules. I'm using these bond lengths in a molecular mechanics force field > (GRID) for flexible ligand docking. I require bond lengths between each atom > type i.e. an aromatic carbon and an sp3 NH group with a lone pair etc etc > > Does anybody know of any resources avialable ? Like a database or websites? > > Any help on this matter would be greatly appreciated > > Cheers > > Peter From chemistry-request@ccl.net Wed Jul 30 21:55:36 2003 Received: from smtp.hotbox.ru (smtp.hotbox.ru [80.68.244.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6V1sH47020391 for ; Wed, 30 Jul 2003 21:55:35 -0400 Received: from verena (verena.ineos.ac.ru [193.233.4.18]) (authenticated bits=0) by smtp.hotbox.ru (8.12.9/8.12.9) with ESMTP id h6V1fduw076064 for ; Thu, 31 Jul 2003 05:41:42 +0400 (MSD) (envelope-from dengolovanov[at]pisem.net) Date: Thu, 31 Jul 2003 05:59:46 +0400 From: dengolovanov X-Mailer: The Bat! (v1.61) Reply-To: dengolovanov X-Priority: 3 (Normal) Message-ID: <95236553475.20030731055946[at]pisem.net> To: chemistry[at]ccl.net Subject: Re: CCL:Standard Bond Lengths? In-Reply-To: <03073012130100.31948@bmbpcu21> References: <03073012130100.31948@bmbpcu21> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Peter, the most reasonable way to solve your problem is to order (or find some one of your friends...) Cambridge Structure Database. You'll find there anythind you want and you may also make statistical analysis halp with it. PO> Hello CCLers, PO> I'm looking for standard bond lengths between various atoms in organic PO> molecules. I'm using these bond lengths in a molecular mechanics force field PO> (GRID) for flexible ligand docking. I require bond lengths between each atom PO> type i.e. an aromatic carbon and an sp3 NH group with a lone pair etc etc PO> Does anybody know of any resources avialable ? Like a database or websites? PO> Any help on this matter would be greatly appreciated PO> Cheers PO> Peter -- Best regards, dengolovanov mailto:dengolovanov[at]pisem.net