From chemistry-request@server.ccl.net Fri Jun 8 06:27:50 2001 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f58ARn506726 for ; Fri, 8 Jun 2001 06:27:49 -0400 Received: by gatekeeper.bnfl.co.uk; id LAA04929; Fri, 8 Jun 2001 11:25:52 +0100 (BST) From: Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma003161; Fri, 8 Jun 01 11:20:29 +0100 Received: from ASN027.bnfl.com (unverified) by ant008.spr.bnfl.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Fri, 8 Jun 2001 10:05:59 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.30.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id KAA06589 for ; Fri, 8 Jun 2001 10:11:10 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.7 (934.1 12-30-1999)) id 00256A65.00383CF7 ; Fri, 8 Jun 2001 10:14:16 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-ID: <00256A65.00383AFC.00@BNotesMTA1.sell.bnfl.com> Date: Fri, 8 Jun 2001 10:14:23 +0000 Subject: Use of 3D crystal data in MOPAC2000 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hi there, I am currently struggling with MOPAC2000 with input of data from a periodic model. Is anyone aware of a package or script that will convert a standard 3D periodic model format (such as .xyz, .car, xtl, etc) into a data set that can be transferred into a MOPAC input file. I have a lot of fairly similar (periodic) structures that I wish to use, and whilst MOPAC2000 claims to have periodic functionality it is very user-unfriendly in this regard. Scott Owens BNFL R&T slo1@bnfl.com From chemistry-request@server.ccl.net Fri Jun 8 04:54:09 2001 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f588s7511275 for ; Fri, 8 Jun 2001 04:54:07 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 8 Jun 2001 10:52:47 +0200 Message-ID: <005c01c0eff8$c735e5e0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <00c301c0e768$a3d56460$320a0a0a@fqspl.com.pl> Subject: Re: CCL:Protein structures Date: Fri, 8 Jun 2001 10:55:33 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f588sA511288 Dear Victor, Beyond chemistry, I am the developer the program Mol2mol (if it is unknown, have a look at for more info: http://www.compuchem.com/mol2mol.htm and/or http://dragon.klte.hu/~gundat/mol2mola.htm ) It started as a chemical file conversion utility but it contains now several utilities to modify the files, among others adding hydrogens automatically taking into consideration pH. During developing I faced several problems, some of them you mentioned as well. I think that by checking manually the hydrogens atom-by-atom only a part of the errors can be eliminated, namely the serious mistakes made during addition of hydrogens (bad torsion angles etc.). When developing the hydrogen addition algorithm, I quickly realized that most of the PDB files contain more or less (depending on the resolution) absolutely incorrect bond lengths. For example, a peptide bond -CO-NH- may contain very short C-N bonds correspondig to a -C(OH)=N- moiety. Now how to deal with it? Assume that it is a PDB file and it is "obviously" a peptide bond? But what if it is a peptide containing unusual substituents and the bond is part of a conjugated system? And so on... Serious "big" modeling programs like Sybyl, Insight etc contain amino acid libraries when adding hydrogens, but this feature cannot help in the case of unusual structural elements. HyperChem can do it only if bond orders are present. Another mistake in pdb files that e.g. some of the carbonyl carbons look clearly pyramidal. So I decided in Mol2mol to add hydrogens "ab initio", and only in the case of problems the algorythm looks that does the residue name "GLU" and atom name "CB" belong to the atom in question? Take it for granted, it is not an easy task. These mistakes, I guess, arise from the uncertainties of the method of structure determination (xray). Therefore the reliability of the position of added hydrogens cannot be higher than that of the heavy atoms. Thus I agree with the others that the most reliable way is that after adding hydrogens a forcefield minimization must be done, and only after it QM. Tamas ----------------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: "Victor Anisimov" To: Sent: Monday, May 28, 2001 1:23 PM Subject: CCL:Protein structures > Dear netters, > > Can someone advise me on the following topic: > > Applying quantum chemical calculations to proteins I always > spend a lot of my time on mechanical preliminary purification > of the protein structures setting hydrogen atoms in proper positions > and checking the structure errors. > > The software that can automate this process is usually not > enough reliable and requires a posteriori expert's check. The > manual correction is tremendously impractical for hundreds of > proteins with thousands of residues that I need to submit for QM > calculation. > > Could you please share with me your experience what software you > consider as the most trustworthy or may be there is some > free or commercially available database of proteins with correct > hydrogen atoms already assigned. What would be your normal > procedure if you would need to submit 50000 atoms' protein for > QM calculation taking the structure from the PDB database? > > My second question is related to protein structure correction > feature of graphical applications that goes beyond adding > hydrogen atoms. > There are many graphical applications that can advise a user to > correct some part of the molecule. To best of my knowledge all > of them are based on the Lewis structure rules. As PDB structures > not always obeying Lewis principles and valence rules the result > of the automatic correction is not reliable enough. > > Could you please recommend me a software free or commercial > if it exists that can safely repair protein structure or can check it > and graphically select those parts of the protein that require > human expertise for correction. Once the user qualified the fragment > as valid the next time check should not suggest this fragment for > correction. > > Thanks for your help, > Victor. > From chemistry-request@server.ccl.net Fri Jun 8 07:00:56 2001 Received: from mailserver.unimi.it ([159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f58B0u508343 for ; Fri, 8 Jun 2001 07:00:56 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id MAA09336; Fri, 8 Jun 2001 12:59:38 +0200 (MET DST) Message-ID: <009001c0f00a$0f2695a0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "Dr. Wolfgang Utz" , Subject: Software for mopac7 Date: Fri, 8 Jun 2001 12:59:15 +0200 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Wolfgang, please look at our VEGA package (http://users.unimi.it/~ddl) that is able to read/write mopac output files (with atomic charges) and it can calculate the MEP surface in several formats. The next VEGA release (OpenGL) will show the surfaces in a 3D graphical engine. Best regards Giulio Vistoli > -- > Dr. Giulio Vistoli > Ist. di Chimica Farmaceutica e Tossicologica > Viale Abruzzi, 42 > I-20131 Milano (Italy) > Tel. +39-02-29502230 > Fax +39-02-29514197 > E-Mail: giulio.vistoli@unimi.it > WWW: http://users.unimi.it/~ddl > From chemistry-request@server.ccl.net Fri Jun 8 11:31:48 2001 Received: from unomail.unomaha.edu ([137.48.1.6]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f58FVl513189 for ; Fri, 8 Jun 2001 11:31:47 -0400 Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 86256A65.00551C52 ; Fri, 8 Jun 2001 10:29:38 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu To: chemistry@ccl.net cc: Roger_Hoburg/CAS/UNO/UNEBR@unomail.unomaha.edu, Edmund_Tisko/CAS/UNO/UNEBR@unomail.unomaha.edu Message-ID: <86256A65.00551AA3.00@unomail.unomaha.edu> Date: Fri, 8 Jun 2001 10:29:32 -0500 Subject: Cyrstal database Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Spartan 5.1 has the ability to import FDAT crystal structures. Does anyone know of data base containing FDAT files of simple lattices such as NaCl or other solids commonly used to introduce crystal structures at the freshmen level? Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Fri Jun 8 16:57:28 2001 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f58KvR519180; Fri, 8 Jun 2001 16:57:27 -0400 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer); Fri, 8 Jun 2001 21:57:33 +0100 Reply-To: "a.oganov" From: "Artem R. Oganov" To: chemistry Cc: chemistry-request Subject: CCL: Superconducting phase transitions Date: Fri, 8 Jun 2001 21:55:13 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all, I would appreciate if you could give me any references to papers or books which would explain why the superconducting phase transitions are always second order. I'd also like to see any experimental papers confirming this conclusion (e.g., by showing the variation of the X-ray diffraction peak intensities). I'll summarise on request. Thanks a lot. Cheers, Artem ----------------------------------------------------- Artem R. Oganov Department of Geological Sciences University College London Gower Street London WC1E 6BT tel: +44 (020)-7679-3344 fax: +44 (020)-7387-1612 email: a.oganov@ucl.ac.uk http://slamdunk.geol.ucl.ac.uk/~artem --------------------------------------------------- From chemistry-request@server.ccl.net Fri Jun 8 17:06:32 2001 Received: from cqf.co.cu ([63.170.172.34]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f58L6N519358 for ; Fri, 8 Jun 2001 17:06:25 -0400 Received: (qmail 15297 invoked from network); 8 Jun 2001 20:55:25 -0000 Received: from unknown (HELO pdc.cqf.co.cu) (10.1.10.2) by 10.1.10.1 with SMTP; 8 Jun 2001 20:55:25 -0000 Received: from cqf.co.cu (PDC [10.1.10.2]) by pdc.cqf.co.cu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id MN7TNPHS; Fri, 8 Jun 2001 05:08:21 -0400 Message-ID: <3B2095F0.B77D2ACA@cqf.co.cu> Date: Fri, 08 Jun 2001 05:08:00 -0400 From: Juan Alexander X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CCL:Hepatic effect References: <3B1F96E1.18745.B4FDC78@localhost> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLs: Thanks to Lawrence Cuffe I will transform my original question, that seems a lot out of topic: I am a computational chemist and I am interested in the modelling of the metabolism effect on drugs. I already have a more or lest steady computational model of drug intake reduction based on oxidative metabolism in the liver for some biochemical paths, and I want to get information on the subject to extend the predictive system to the whole (or a bigger part at least) problem, as well as know if there is another computational chemistry colleague working on the subject. Greatings and thanks again to Lawrence Prof. Juan Alexander Padron Garcia Centro de Quimica Farmaceutica La Havana, Cuba Tel. 285109 padrongj@cqf.co.cu From chemistry-request@server.ccl.net Fri Jun 8 10:59:08 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f58Ex7512749 for ; Fri, 8 Jun 2001 10:59:07 -0400 Received: from chad (128.196.86.119) by deimos.email.Arizona.EDU (5.1.056) id 3B1F83D900015EA9 for chemistry@ccl.net; Fri, 8 Jun 2001 07:59:06 -0700 Message-ID: <004601c0f02b$a416ee00$7756c480@chem.arizona.edu> From: "cmrisko" To: Subject: G98 Error -- Replies Date: Fri, 8 Jun 2001 07:59:39 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0043_01C0EFF0.F7A74D20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0043_01C0EFF0.F7A74D20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thank you all for the assistance. I have retried the set of = calculations with the additions of scf=3Dnovaracc and int=3Dultrafine = with success. Below, find copies of the suggestions that were sent as = well as the original message. SUGGESTIONS: When using B3LYP ( and I believe DFT in general) the Gaussian = integration procedure can loose track of some of the electron density. = When the amount lost exceeds a threshold the program crashes. This can = sometimes be fixed by using SCF=3D(Tight, NoVaracc) in the input line. = This means that integrations are fully calculated at all times as = opposed to being approximated some of the time. Calculation time is = increased but the jobs usually complete, good luck,=20 Sean=20 (Sean O'brien) Hello, I haven't understood what is behind this problem but I solve it like this: a) # scf(novaracc) int(grid=3Dultrafine) if this doesn't work, =20 b) run single point HF calculation # scf(tight,novaracc) =20 and then # guess(read) b3lyp=20 or # guess(read) b3lyp int(grid=3Dultrafine) (sometimes this works) if this doesn't work c) switch off the symmetry if this doesn't work....try somethig else...:) Greetings MSS --=20 I------------------------------------------------------------------------= ----I I Michal Straka Telephone: 358-9-191 50173 = I I Department of Chemistry Secretary: 358-9-191 50170 = I I P.O.B. 55 (A.I. Virtasen aukio 1) FAX: 358-9-191 50169 = I I FIN-00014 Helsinki E-mail: straka@chem.helsinki.fi = I I Finland = http://www.chem.helsinki.fi/~straka I I------------------------------------------------------------------------= ----I hello: I believe this message means that the integrated density (which = should equal the number of electrons) does not equal the number of = electrons, so it is inconsistant. The first thing I would try is to run = the same calculation in another basis. It may result from an numerical = instability.=20 =20 --=20 Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona I guess it is just one of the rubbisch Gaussian integration grids.=20 Are you using atoms beyond Argon? --=20 +---------------------------------+-------------------------------------+= | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 = | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 = | | Strasse des 17. Juni 135 | eMail = | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De = | +---------------------------------+-------------------------------------+= This is a very unusual error to get with your straightforward input,=20 so I'd rather not speculate on the cause until I've done some debugging. = Can you send me your full input and output files? Thanks. Regards, Jim Hess ORIGINAL MESSAGE: Good Day! I hope all is going well. I have a question pertaining to an = error message that I receive during geometry optimization with a = particular molecule (basically two, six-memeber rings). My input lines = are such: #P b3lyp/6-31G(d) IOP(99/14=3D1) Opt=3Dz-matrix And, the error message that I receive is: Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Cycle 2 Pass 1 IDiag 1: Warning! Spurious integrated density: NE=3D 100 NElCor=3D 0 Integral=3D -748.37012 = Tolerance=3D1.00D-03 Consistency failure #2 in CalDSu. Error termination=20 Everything appears to be running smoothly (converging) up to this = point...then it terminates.=20 Any help would be greatly appreciated. Thanks in advance. Chad=20 ++++++++++++++++++++++++++++++ Chad Risko Graduate Student Department of Chemistry University of Arizona ++++++++++++++++++++++++++++++ ------=_NextPart_000_0043_01C0EFF0.F7A74D20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Thank you all for the assistance.  = I have=20 retried the set of calculations with the additions of scf=3Dnovaracc and = int=3Dultrafine with success.  Below, find copies of the = suggestions that=20 were sent as well as the original message.
 
SUGGESTIONS:
When using  B3LYP ( and I believe = DFT in=20 general) the Gaussian integration procedure can loose track of some of = the=20 electron density. When the amount lost exceeds a threshold the program = crashes. This can sometimes be fixed by using  SCF=3D(Tight, = NoVaracc) in=20 the input line. This means that integrations are fully calculated at = all times=20 as opposed to being approximated some of the time. Calculation time is = increased but the jobs usually complete,
good luck,=20

Sean
(Sean O'brien)

Hello,
I haven't understood what is behind this problem
but I = solve it=20 like this:
a) # scf(novaracc) int(grid=3Dultrafine)

if this = doesn't=20 work, 

b) run single point HF calculation #=20 scf(tight,novaracc)
 
and then  # guess(read) b3lyp=20
    or    # guess(read) b3lyp=20 int(grid=3Dultrafine)

(sometimes this works) if this doesn't = work

c)=20 switch off the symmetry

if this doesn't work....try somethig=20 else...:)
Greetings
MSS
--=20
I--------------------------------------------------------------------= --------I
I=20 Michal=20 Straka           &= nbsp;          =20 Telephone: 358-9-191=20 50173           &n= bsp;=20 I
I Department of=20 Chemistry          &nbs= p; =20 Secretary: 358-9-191=20 50170           &n= bsp;=20 I
I P.O.B. 55 (A.I. Virtasen aukio 1)  =20 FAX:       358-9-191=20 50169           &n= bsp;=20 I
I FIN-00014=20 Helsinki           = ;      =20 E-mail:    straka@chem.helsinki.fi =    =20 I
I=20 Finland           =             &= nbsp;    =20 http://www.chem.helsinki.fi/= ~straka   =20 I
I-------------------------------------------------------------------= ---------I

hello:

    I believe this message means that the integrated = density=20 (which should equal the number of electrons) does not equal the number = of=20 electrons, so it is inconsistant. The first thing I would try is to run = the same=20 calculation in another basis. It may result from an numerical = instability.=20
  

-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
            &=
nbsp;        and Computational
            &=
nbsp;        Quantum Chemistry
Department of Chemistry
University of Arizona

I guess it is just one of the rubbisch Gaussian integration grids. =
Are=20 you using atoms beyond Argon?
--=20
+---------------------------------+----------------------------------= ---+
|=20 Prof. Christoph van Wullen      | Tele-Phone = (+49)=20 (0)30 314 27870    |
| Technische Universitat Sekr. C3 = |=20 Tele-Fax   (+49) (0)30 314 23727    |
| = Strasse des=20 17. Juni 135        |=20 eMail           &n= bsp;           &nb= sp;      =20 |
| D-10623 Berlin, = Germany         |=20 Christoph.vanWullen@TU-B= erlin.De   =20 |
+---------------------------------+---------------------------------= ----+

 

This is a very unusual error to get with your straightforward input, =
so=20 I'd rather not speculate on the cause until I've done some debugging. =
Can=20 you send me your full input and output files? = Thanks.

Regards,
Jim=20 Hess

ORIGINAL MESSAGE:

Good Day!  I hope all is going = well.  I=20 have a question pertaining to an error message that I receive during = geometry=20 optimization with a particular molecule (basically two, six-memeber=20 rings).  My input lines are such:
       #P=20 b3lyp/6-31G(d)
         &= nbsp; =20 IOP(99/14=3D1)
   =         =20 Opt=3Dz-matrix
 
And, the error message that I receive=20 is:
 
     Problem = detected with=20 inexpensive integrals.
     Switching to full = accuracy=20 and repeating last cycle.
     Cycle   = 2 =20 Pass 1  IDiag 1:
     Warning!  = Spurious=20 integrated density:
     NE=3D  100=20 NElCor=3D    0 Integral=3D -748.37012=20 Tolerance=3D1.00D-03
     Consistency failure #2 = in=20 CalDSu.
     Error termination 
Everything appears to be running = smoothly=20 (converging) up to this point...then it terminates. 
 
Any help would be greatly = appreciated.  Thanks=20 in advance.
 
Chad
++++++++++++++++++++++++++++++
Chad=20 Risko
Graduate Student
Department of Chemistry
University of=20 Arizona
++++++++++++++++++++++++++++++
------=_NextPart_000_0043_01C0EFF0.F7A74D20--