From owner-chemistry@ccl.net Tue Apr 28 00:12:00 2009 From: "UZMA MAHMOOD mehmoodchemist---gmail.com" To: CCL Subject: CCL: GOLD_docking Message-Id: <-39184-090427225909-20694-MpwXBd0KjV+GnmR/KE8sCw-x-server.ccl.net> X-Original-From: UZMA MAHMOOD Content-Type: multipart/alternative; boundary=000e0cd17b9aa2a188046894a4d7 Date: Tue, 28 Apr 2009 07:58:53 +0500 MIME-Version: 1.0 Sent to CCL by: UZMA MAHMOOD [mehmoodchemist~!~gmail.com] --000e0cd17b9aa2a188046894a4d7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear VL Thanks for your reply yeah exactly you are right and i was also quite conscious about the input file for performing the job on GOLD software and care all the possible parameters, procedures and keenly look the input files but still lack something i had already done all the your advices steps and one thing more i also run the calculation without specify the covalent interaction nothing error showed done smoothly............ but showing error in covalent interaction regards uzma On Sun, Apr 26, 2009 at 10:58 PM, Vincent.Leroux~~loria.fr < owner-chemistry _ ccl.net> wrote: > > Sent to CCL by: Vincent.Leroux##loria.fr > Hi Uzma, > > GOLD is very sensitive to input data consistency. You can run into numero= us > problems, but I would first suggest you read the output log files. These = are > particularly detailed and informative so take your time. > > Some general advices > > - Is everything, target and ligands, protonated correctly? > > - Try to perform the calculation simply without the covalent bond > definition. If it launches fine, then you know exactly where the problem = is. > > - If your target protein is given as a PDB file, then GOLD converts it > automatically to MOL2 before processing it. Never did covalent docking > myself, but I would suggest, in such a case, double-checking the atom > numbers between the input and generated protein.mol2, as a mismatch might > translate to the covalent bond definition... > > - Make sure that your input ligands are in MOL2 format, and that the atom > types are correct. GOLD makes use of some non-standard definitions, there= is > an entire section in the manual for that, check it out. > > VL > > > > "uzma mahmood mehmoodchemist[*]gmail.com" a > =E9crit : > > >> Sent to CCL by: "uzma mahmood" [mehmoodchemist##gmail.com] >> dear all subscriber >> >> any one can help me regarding docking on gold software by using covalent >> interaction all apply all the procedure as define in manual but i think = i >> have some problem in input files so any one who has done this type of wo= rk >> so kindly help me resolve this problem >> >> >> thanks >> >> uzma >> >> > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --=20 Uzma Mahmood, Junior Research Fellow, International Center of Chemical and biological Sciences (ICCBS). --000e0cd17b9aa2a188046894a4d7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear VL

Thanks for your reply

yeah exactly you are ri= ght and i was also quite conscious about the input file for performing the = job on GOLD software and care all the possible parameters, procedures and k= eenly look the input files but still lack something
i had already done all the your advices steps and one thing more i also run= the calculation without specify the covalent interaction nothing error sho= wed done smoothly............ but showing error in covalent interaction


regards


uzma

On Sun, A= pr 26, 2009 at 10:58 PM, Vincent.Leroux~~loria.= fr <own= er-chemistry _ ccl.net> wrote:

Sent to CCL by: Vincent.Leroux##loria.fr
Hi Uzma,

GOLD is very sensitive to input data consistency. You can run into numerous= problems, but I would first suggest you read the output log files. These a= re particularly detailed and informative so take your time.

Some general advices

- Is everything, target and ligands, protonated correctly?

- Try to perform the calculation simply without the covalent bond definitio= n. If it launches fine, then you know exactly where the problem is.

- If your target protein is given as a PDB file, then GOLD converts it auto= matically to MOL2 before processing it. Never did covalent docking myself, = but I would suggest, in such a case, double-checking the atom numbers betwe= en the input and generated protein.mol2, as a mismatch might translate to t= he covalent bond definition...

- Make sure that your input ligands are in MOL2 format, and that the atom t= ypes are correct. GOLD makes use of some non-standard definitions, there is= an entire section in the manual for that, check it out.

VL



"uzma mahmood mehmoodchemist[*]gmail.com" <owner-chemistry:-:ccl.net> a =E9crit=A0:


Sent to CCL by: "uzma =A0mahmood" [mehmoodchemist##gmail.com]
dear all subscriber

any one can help me regarding docking on gold software by using covalent in= teraction all apply all the procedure as define in manual but i think i hav= e some problem in input files so any one who has done this type of work so = kindly help me resolve this problem


thanks

uzma




- This is automatically added to each message by the mailing script -
E-mail to subscribers: CHEMISTRY _ ccl.net or use:
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http://www.ccl.net/chemistry/sub_unsub.shtml=

Before posting, check wait time at: http://www.ccl.net

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--
Uzma Mahmood,
Junior= Research Fellow,
International Center of Chemical and biological Scienc= es (ICCBS).
--000e0cd17b9aa2a188046894a4d7-- From owner-chemistry@ccl.net Tue Apr 28 03:51:01 2009 From: "Michel Petitjean petitjean.chiral]=[gmail.com" To: CCL Subject: CCL: Programs for molecular surface calculations and a question about QCPE Message-Id: <-39185-090428034746-2685-yTEsPAc3GHU4n7TgQSqFwA~~server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Apr 2009 09:47:17 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%%gmail.com] Hi Marc, If you need an accurate result (e.g. for numerical differentiation purposes), an exact analytical calculation is required. ASV does that (http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html), assuming that you have fixed all van der Waals radii. Remarks: the surfaces are highly sensitive to the radii values (volumes are much less sensitive). I neglect the problems arising from flexibility. If an approximate result suffices (precision, say, 0.01 A^2), the Monte-Carlo method runs faster, particularly when there are many atoms (hundreds or thousands). The Monte-Carlo methods are also in ASV, and the source routines are downloadable for free from the same web page. About the normals: They are implicitely known from van der Waals spheres. If you prefer to consider the mesh induced by the Monte-Carlo method, you need to triangulate a non convex solid. Let N be the number of atomic spheres. Here, I would suggest to generate points on the surface of each sphere via the Monte-Carlo method, then to generate the N convex hulls (this task can be parallelized; RADI2 computes convex hulls and is available on the same web page than ASV), then to compute the union of these polyhedral hulls (needs to compute the intersection of 3D triangles, etc.). This latter task is O(N^2) time consuming, and I do not know if it can be parallelized efficiently. The global computing time depends mainly of the number of atoms and on the number of vertices you generate. Nothing difficult in programming all that, but it may take time if you are not fluent with convex hulls and other euclidean geometry programs. Other suggestion: have you looked at the INRIA if there are such library programs (may be in CGAL, I do not know). Good luck. Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean.~~.cea.fr, petitjean.chiral.~~.gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.html ---------- Forwarded message ---------- > From: Marc Baaden baaden(!)smplinux.de Date: 2009/4/28 Subject: CCL: Programs for molecular surface calculations and a question about QCPE Sent to CCL by: "Marc Baaden" [baaden---smplinux.de] Dear CCL, I am currently looking for programs performing molecular surface calculations. Of course there are lots of them as well as a wealth of algorithms. I do however have a number of restrictions which seem to limit the number of candidates (I haven't found any so far..): - I want to use the software within another (open-source) project, so source should be available, modifiable and redistributable - performance is very important - parallelisation/parallelizability would be great - approximation is acceptable - the code should determine a mesh, ie vertices, faces and normals I'd be very grateful for any suggestions. Thank you in advance! Marc Baaden By the way, I was also testing programs referred to in publications etc. and one of those is MSEED. It is supposed to be available via QCPE, but I actually couldn't find any working webpage with access to QCPE programs. Has QCPE disappeared? From owner-chemistry@ccl.net Tue Apr 28 08:50:00 2009 From: "Michel Petitjean petitjean.chiral]|[gmail.com" To: CCL Subject: CCL: Chemoinformatics workshop, Montpellier 24-25 June 2009 / Reminder Message-Id: <-39186-090428084614-3661-0/zvI31llJ7P3B287VHDUA- -server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Apr 2009 13:49:29 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral-,-gmail.com] Dear CCLers, The SFCi (Societe Francaise de Chemoinformatique) organizes a chemoinformatics workshop in Montpellier (France), 24-25 June 2009. A part of the oral communications will be in French, but some will be in English. Please visit: http://www.univ-orleans.fr/GFC/journee2009.html Thanks. Michel Petitjean, SFCi, General Secretary, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean ~ cea.fr, petitjean.chiral ~ gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html From owner-chemistry@ccl.net Tue Apr 28 11:17:00 2009 From: "Narayan Chandra Bera ncbera05%a%gmail.com" To: CCL Subject: CCL: Kindly solve my Turbomol problem Message-Id: <-39187-090427161426-19134-vUj9ao/bmCOvsyPgPzfTGQ*o*server.ccl.net> X-Original-From: Narayan Chandra Bera Content-Type: multipart/alternative; boundary=0016e6461678771a6e04688efd53 Date: Mon, 27 Apr 2009 13:14:13 -0700 MIME-Version: 1.0 Sent to CCL by: Narayan Chandra Bera [ncbera05.:.gmail.com] --0016e6461678771a6e04688efd53 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Sir, I am a turbomol user, I am doing single point energy calculation of a molecule having 43 atoms, its charge is -1 and multiplicity is 1 at RI-MP2/aug-cc-pVTZ level . To perform this ri-mp2 calculation i did dscf calculation and all the necessary input through define comment, the dscf calculation has been performed successfully but problem arises in rimp2 calculation during calculation, after calculating some steps it stopped automatically without giving any error massage (please see below, i'm giving the last few lines). I cant understand whats the problem. Kindly help me. Waiting for your reply. With best regards, Narayan echeck from tr(Qit) mp2 energy difference between galoop and gamder=-0.1243449787580D-13 ----------------------------------------------------- prepare right hand side of z-vector equations ----------------------------------------------------- total memory allocated for eval. of r.h.s. of z-vector equation : 51 MByte disc space (kbyte) allocation for 1 2e-integral file(s) : -------------------------------------------------------- twoint 0 -------------------------------------------------------- maximum number of buffers which may be written onto 2e-file(s) = 0 0 2 e - integrals written in 0 blocks requiring 0 k-byte total zprep cpu-time : 4 hours 44 minutes and 58 seconds total zprep wall-time : 4 hours 45 minutes and 18 seconds additional memory allocated for solution of z-vector equation : 17 MByte ------------------------------------------------- -CPHF- contribution to MP2-Gradient via Z-vector ------------------------------------------------- Requested convergence is 0.1000000000E-10 RMS and a residual norm of 0.1000000000E-02 Iteration RMS |R| 1 0.6245080095E-06 0.2526108240E+00 2 0.5572694041E-07 0.7545978248E-01 3 0.1043855378E-07 0.3265901752E-01 4 0.1252709341E-08 0.1131378984E-01 5 0.1215664530E-09 0.3524437567E-02 6 0.1871648610E-10 0.1382913790E-02 rimp2.out lines 777-821/821 (END) -- ********************************************************** Dr. Narayan Chandra Bera Postdoctoral Research Associate USA ------------------------------------------------------------------------ --0016e6461678771a6e04688efd53 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir,
=A0=A0 =A0 =A0 =A0 =A0I am a turbomol user, I am doing single= point energy calculation of a molecule having 43 atoms, its charge is -1 a= nd multiplicity is 1 at RI-MP2/aug-cc-pVTZ level . To perform this ri-mp2 c= alculation i did dscf calculation and all the necessary input through defin= e comment, the dscf calculation has been performed successfully but problem= arises in rimp2 calculation during calculation, after calculating some ste= ps it stopped automatically without giving any error massage (please see be= low, i'm giving the last few lines). I cant understand whats the proble= m. Kindly help me. Waiting for your reply.

With best regards,
Narayan
=A0=A0 = =A0

=A0echeck from tr(Qit)
=A0m= p2 energy difference between galoop and gamder=3D-0.1243449787580D-13
=

=A0-----------------------------------------------------
=A0=A0 =A0 prepare right hand side of z-vector equations
=A0--= ---------------------------------------------------

=A0total memory allocated for eval. of r.h.s. of z-vector equation : =A0 = 51 MByte

=A0=A0 disc space (kbyte) allocation for =A01 2e-integr= al file(s) :
=A0=A0 ---------------------------------------------= -----------
=A0=A0 twoint =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0
=A0=A0 --------------------------------------------------------
<= div>
=A0maximum number of buffers which may be written onto 2= e-file(s) =3D =A0 =A0 =A0 =A0 0


=A0= =A0 =A0 =A0 =A0 0 2 e - integrals written in =A0 =A0 =A0 =A0 0 blocks requi= ring =A0 =A0 =A0 0 k-byte

=A0=A0 =A0 =A0 =A0 total =A0zprep =A0cpu-time : =A04 ho= urs 44 minutes and 58 seconds
=A0=A0 =A0 =A0 =A0 total =A0zprep w= all-time : =A04 hours 45 minutes and 18 seconds
=A0additional mem= ory allocated for solution of z-vector equation : =A0 17 MByte

=A0=A0 =A0 =A0 =A0 =A0---------------------------------= ----------------
=A0=A0 =A0 =A0 =A0 =A0-CPHF- contribution to MP2= -Gradient via Z-vector
=A0=A0 =A0 =A0 =A0 =A0--------------------= -----------------------------

=A0=A0 Requested convergence is =A0 =A0 0.1000000000E-1= 0 =A0RMS
=A0=A0 =A0 and a residual norm of =A0 =A0 0.1000000000E-= 02

=A0=A0 =A0 =A0Iteration =A0 =A0 =A0 =A0 =A0 RMS= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 |R|

=A0=A0 =A0 =A0 =A0 =A0 1 =A0 =A0 =A0 =A00.6245080095E-06 =A0 =A0= =A00.2526108240E+00
=A0=A0 =A0 =A0 =A0 =A0 2 =A0 =A0 =A0 =A00.55= 72694041E-07 =A0 =A0 =A00.7545978248E-01
=A0=A0 =A0 =A0 =A0 =A0 3= =A0 =A0 =A0 =A00.1043855378E-07 =A0 =A0 =A00.3265901752E-01
=A0= =A0 =A0 =A0 =A0 =A0 4 =A0 =A0 =A0 =A00.1252709341E-08 =A0 =A0 =A00.11313789= 84E-01
=A0=A0 =A0 =A0 =A0 =A0 5 =A0 =A0 =A0 =A00.1215664530E-09 =A0 =A0 =A00.= 3524437567E-02
=A0=A0 =A0 =A0 =A0 =A0 6 =A0 =A0 =A0 =A00.18716486= 10E-10 =A0 =A0 =A00.1382913790E-02
rimp2.out lines 777-821/821 (E= ND)






--
******= ****************************************************
Dr. Narayan Chandra= Bera
Postdoctoral Research Associate
USA
------------------------= ------------------------------------------------

--0016e6461678771a6e04688efd53-- From owner-chemistry@ccl.net Tue Apr 28 11:52:00 2009 From: "vadicherla tati reddy tatireddy.vadicherla^-^gmail.com" To: CCL Subject: CCL: Any Freely avaliable NaturalProduct Database for Download Message-Id: <-39188-090428052921-4697-ofpkhNDYzxiXdESuqv+NBA:+:server.ccl.net> X-Original-From: vadicherla tati reddy Content-Type: multipart/alternative; boundary=0016362835b65e1a4704689a1868 Date: Tue, 28 Apr 2009 14:59:09 +0530 MIME-Version: 1.0 Sent to CCL by: vadicherla tati reddy [tatireddy.vadicherla]*[gmail.com] --0016362835b65e1a4704689a1868 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All, Is there any Freely avaliable Natural Product database in ( sdf,mol,smi )format for download... if yes can u plz mail me the link.... Thanks TatiReddy --0016362835b65e1a4704689a1868 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi All,
=A0
Is there any=A0Freely avaliable Natural Product database in ( sdf,mol,= smi )format for download... if yes can u plz=A0mail me the link....
=A0
=A0
=A0
=A0
Thanks
TatiReddy=A0
--0016362835b65e1a4704689a1868-- From owner-chemistry@ccl.net Tue Apr 28 14:14:00 2009 From: "Abdul Hameed, MohamedDiwanMo mabdu3*_*email.uky.edu" To: CCL Subject: CCL: Any Freely avaliable NaturalProduct Database for Download Message-Id: <-39189-090428141135-11773-pzT5OgVGz/sw5S9TD+XpSQ::server.ccl.net> X-Original-From: "Abdul Hameed, MohamedDiwanMo" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_62D3F106CB16C34D825A1B75EFBA68390180D95689EX7FM04adukye_" Date: Tue, 28 Apr 2009 13:37:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Abdul Hameed, MohamedDiwanMo" [mabdu3[]email.uky.edu] --_000_62D3F106CB16C34D825A1B75EFBA68390180D95689EX7FM04adukye_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, Check in ZINC database subsets: http://zinc.docking.org/vendor0/ 'ZINC natural product' is the name of the subset. Cheers, Mohamed Diwan College of Pharmacy University of Kentucky. ________________________________ > From: owner-chemistry+mabdu3=3D=3Demail.uky.edu-$-ccl.net [mailto:owner-chemi= stry+mabdu3=3D=3Demail.uky.edu-$-ccl.net] On Behalf Of vadicherla tati reddy = tatireddy.vadicherla^-^gmail.com Sent: Tuesday, April 28, 2009 5:29 AM To: Abdul Hameed, MohamedDiwanMo Subject: CCL: Any Freely avaliable NaturalProduct Database for Download Hi All, Is there any Freely avaliable Natural Product database in ( sdf,mol,smi )fo= rmat for download... if yes can u plz mail me the link.... Thanks TatiReddy --_000_62D3F106CB16C34D825A1B75EFBA68390180D95689EX7FM04adukye_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

Check in ZINC databa= se subsets:

 

http://zinc.docking.org/vendor0/<= /a>

 

‘ZINC natural product’ is the name of the subset.

 

Cheers,

Mohamed Diwan

College of Pharmacy<= o:p>

University of Kentuc= ky.

From:= owner-chemistry+mabdu3=3D=3Demail.uky.edu-$-ccl.net [mailto:owner-chemistry+mabdu3=3D=3Demail.uky.edu-$-ccl.net] On Behalf Of vadicherla tati reddy tatireddy.vadicherla^-^gmail.com
Sent: Tuesday, April 28, 200= 9 5:29 AM
To: Abdul Hameed, MohamedDiw= anMo
Subject: CCL: Any Freely ava= liable NaturalProduct Database for Download<= /o:p>

 

Hi All,

 

Is there any Freely avaliable Natural Produ= ct database in ( sdf,mol,smi )format for download... if yes can u plz mai= l me the link....

 

 

 

 

Thanks

TatiReddy 

--_000_62D3F106CB16C34D825A1B75EFBA68390180D95689EX7FM04adukye_-- From owner-chemistry@ccl.net Tue Apr 28 17:28:00 2009 From: "Shuping Huang huangshp]-[fjirsm.ac.cn" To: CCL Subject: CCL:G: error in qst2 calculations in Gauss Message-Id: <-39190-090428113532-18628-nDXR3C1IR8e46YpYpRaNqg^_^server.ccl.net> X-Original-From: "Shuping Huang" Date: Tue, 28 Apr 2009 11:35:27 -0400 Sent to CCL by: "Shuping Huang" [huangshp,fjirsm.ac.cn] Dear all, I used qst2 to find transition state. The input file is as follows: %mem=500mb %nproc=4 #p opt=(qst2,maxcycle=500) freq mp2/6-31g(d) geom=connectivity scf=maxcycle=800 The job failed. The error message is as follws: Iteration100 RMS(Cart)= 0.00007251 RMS(Int)= 0.18458671 New curvilinear step not converged. ***** Convergence failure in GTrans ***** Try using 3 structures as input for QST transition state search Error termination via Lnk1e in /usr/local/bin/g03/l101.exe at Tue Apr 28 22:56:06 2009. Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 1 Scr= 1 Any suggestio would be highly apriciated. From owner-chemistry@ccl.net Tue Apr 28 18:03:00 2009 From: "Robert Wolf r.wolf~!~uni-muenster.de" To: CCL Subject: CCL:G: problem calculating NLMOs Message-Id: <-39191-090428131407-6786-Qy34UurLqywvJgettWgPGg++server.ccl.net> X-Original-From: "Robert Wolf" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01C9C82E.4AA8D840" Date: Tue, 28 Apr 2009 18:22:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Robert Wolf" [r.wolf||uni-muenster.de] This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C9C82E.4AA8D840 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL subscribers, =20 I'm trying to calculate the NLMOs of a phosphorus cage compound using = NBO3.1 implemented in Gaussianl. However, I receive the following error = message: =20 NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS: =20 Highest occupied NBOs are not at the beginning of the NBO list; The NLMO program is not currently set up to handle this. Illegal range for read: IUnit=3D 7 Address=3D -256 Length=3D -256 File length=3D 1574400. Error termination in NtrErr: NtrErr called from NtrIO. Has anyone experience with this problem? =20 Kind regards, Robert =20 -- Dr. Robert Wolf Institut f=FCr Anorganische und Analytische Chemie WWU M=FCnster Corrensstra=DFe 30 D-48149 M=FCnster Germany http://www.uni-muenster.de/Chemie.ac/uhl/wolf.html Tel. +49 251 83-36090 (office) / -36070 (lab), FAX +49 251 83-36660 (office Prof. Uhl) =20 _____ =20 Von: owner-chemistry+r.wolf=3D=3Duni-muenster.de_+_ccl.net [mailto:owner-chemistry+r.wolf=3D=3Duni-muenster.de_+_ccl.net] Im Auftrag = von Narayan Chandra Bera ncbera05%a%gmail.com Gesendet: Montag, 27. April 2009 22:14 An: Wolf, Robert Betreff: CCL: Kindly solve my Turbomol problem Dear Sir,=20 I am a turbomol user, I am doing single point energy = calculation of a molecule having 43 atoms, its charge is -1 and multiplicity is 1 at RI-MP2/aug-cc-pVTZ level . To perform this ri-mp2 calculation i did dscf calculation and all the necessary input through define comment, the dscf calculation has been performed successfully but problem arises in rimp2 calculation during calculation, after calculating some steps it stopped automatically without giving any error massage (please see below, i'm = giving the last few lines). I cant understand whats the problem. Kindly help = me. Waiting for your reply. With best regards, Narayan =20 echeck from tr(Qit) mp2 energy difference between galoop and gamder=3D-0.1243449787580D-13 ----------------------------------------------------- prepare right hand side of z-vector equations ----------------------------------------------------- total memory allocated for eval. of r.h.s. of z-vector equation : 51 MByte disc space (kbyte) allocation for 1 2e-integral file(s) : -------------------------------------------------------- twoint 0 -------------------------------------------------------- maximum number of buffers which may be written onto 2e-file(s) =3D = 0 0 2 e - integrals written in 0 blocks requiring 0 k-byte total zprep cpu-time : 4 hours 44 minutes and 58 seconds total zprep wall-time : 4 hours 45 minutes and 18 seconds additional memory allocated for solution of z-vector equation : 17 = MByte ------------------------------------------------- -CPHF- contribution to MP2-Gradient via Z-vector ------------------------------------------------- Requested convergence is 0.1000000000E-10 RMS and a residual norm of 0.1000000000E-02 Iteration RMS |R| 1 0.6245080095E-06 0.2526108240E+00 2 0.5572694041E-07 0.7545978248E-01 3 0.1043855378E-07 0.3265901752E-01 4 0.1252709341E-08 0.1131378984E-01 5 0.1215664530E-09 0.3524437567E-02 6 0.1871648610E-10 0.1382913790E-02 rimp2.out lines 777-821/821 (END) --=20 ********************************************************** Dr. Narayan Chandra Bera Postdoctoral Research Associate USA ------------------------------------------------------------------------ ------=_NextPart_000_001C_01C9C82E.4AA8D840 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCL subscribers,
 
I'm trying to calculate the NLMOs of = a phosphorus=20 cage compound using NBO3.1 implemented in Gaussianl. However, I = receive the=20 following error message:
 
NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO)=20 ANALYSIS:
 
 Highest occupied NBOs are not at the = beginning of the=20 NBO list;
 The NLMO program is not currently set up to handle=20 this.
 Illegal range for read:  IUnit=3D  7=20 Address=3D      -256=20 Length=3D          &nbs= p; -256=20 File length=3D        =20 1574400.
 Error termination in NtrErr:
 NtrErr called = > from=20 NtrIO.
Has anyone experience with this=20 problem?
 
Kind regards,
Robert
 

--
Dr. Robert Wolf
Institut f=FCr Anorganische = und=20 Analytische Chemie
WWU M=FCnster

Corrensstra=DFe 30
D-48149 = M=FCnster
Germany

http://www.un= i-muenster.de/Chemie.ac/uhl/wolf.html

Tel. =20 +49 251 83-36090 (office) / -36070 (lab),
FAX +49 251 83-36660 = (office Prof.=20 Uhl)

 

Von:=20 owner-chemistry+r.wolf=3D=3Duni-muenster.de_+_ccl.net=20 [mailto:owner-chemistry+r.wolf=3D=3Duni-muenster.de_+_ccl.net] Im = Auftrag von=20 Narayan Chandra Bera ncbera05%a%gmail.com
Gesendet: = Montag, 27.=20 April 2009 22:14
An: Wolf, Robert
Betreff: = CCL:=20 Kindly solve my Turbomol problem

Dear Sir,
          I am a turbomol user, I am = doing=20 single point energy calculation of a molecule having 43 atoms, its = charge is -1=20 and multiplicity is 1 at RI-MP2/aug-cc-pVTZ level . To perform this = ri-mp2=20 calculation i did dscf calculation and all the necessary input through = define=20 comment, the dscf calculation has been performed successfully but = problem arises=20 in rimp2 calculation during calculation, after calculating some steps it = stopped=20 automatically without giving any error massage (please see below, i'm = giving the=20 last few lines). I cant understand whats the problem. Kindly help me. = Waiting=20 for your reply.

With best regards,
Narayan
    

 echeck from tr(Qit)
 mp2 energy difference between galoop and=20 gamder=3D-0.1243449787580D-13

 -----------------------------------------------------
     prepare right hand side of z-vector = equations
 -----------------------------------------------------

 total memory allocated for eval. of r.h.s. of z-vector = equation :=20   51 MByte

   disc space (kbyte) allocation for  1 2e-integral = file(s)=20 :
   = --------------------------------------------------------
   twoint             =    =20                     =  =20           0
   = --------------------------------------------------------

 maximum number of buffers which may be written onto = 2e-file(s) =3D=20         0


         0 2 e - integrals written in =  =20       0 blocks requiring       0 = k-byte

         total  zprep  cpu-time = :=20  4 hours 44 minutes and 58 seconds
         total  zprep wall-time : =  4=20 hours 45 minutes and 18 seconds
 additional memory allocated for solution of z-vector equation = :=20   17 MByte

        =20  -------------------------------------------------
          -CPHF- contribution to = MP2-Gradient=20 via Z-vector
        =20  -------------------------------------------------

   Requested convergence is     = 0.1000000000E-10=20  RMS
     and a residual norm of    =20 0.1000000000E-02

      Iteration         =   RMS=20                   |R|

           1      =20  0.6245080095E-06      0.2526108240E+00
           2      =20  0.5572694041E-07      0.7545978248E-01
           3      =20  0.1043855378E-07      0.3265901752E-01
           4      =20  0.1252709341E-08      0.1131378984E-01
           5      =20  0.1215664530E-09      0.3524437567E-02
           6      =20  0.1871648610E-10      0.1382913790E-02
rimp2.out lines 777-821/821 (END)






-- =
**********************************************************
Dr.=20 Narayan Chandra Bera
Postdoctoral Research=20 Associate
USA
-----------------------------------------------------= -------------------

------=_NextPart_000_001C_01C9C82E.4AA8D840-- From owner-chemistry@ccl.net Tue Apr 28 23:40:01 2009 From: "Dr Ponnadurai Ramasami ramchemi]![intnet.mu" To: CCL Subject: CCL:G: error in qst2 calculations in Gauss Message-Id: <-39192-090428232602-13380-JuTdBQlAwEamcQk8duHl8A!A!server.ccl.net> X-Original-From: "Dr Ponnadurai Ramasami" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 29 Apr 2009 07:25:31 +0500 MIME-Version: 1.0 Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi##intnet.mu] Huang Try qst3 see Gaussian manual for more details all the best Ramasami ----- Original Message ----- > From: "Shuping Huang huangshp]-[fjirsm.ac.cn" To: "Ramasami, Ponnadurai " Sent: Tuesday, April 28, 2009 8:35 PM Subject: CCL:G: error in qst2 calculations in Gauss > > Sent to CCL by: "Shuping Huang" [huangshp,fjirsm.ac.cn] > Dear all, > I used qst2 to find transition state. The input file is as follows: > %mem=500mb > %nproc=4 > #p opt=(qst2,maxcycle=500) freq mp2/6-31g(d) geom=connectivity > scf=maxcycle=800 > > > The job failed. The error message is as follws: > Iteration100 RMS(Cart)= 0.00007251 RMS(Int)= 0.18458671 > New curvilinear step not converged. > ***** Convergence failure in GTrans ***** > Try using 3 structures as input for > QST transition state search > Error termination via Lnk1e in /usr/local/bin/g03/l101.exe at Tue Apr 28 > 22:56:06 2009. > Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds. > File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Any suggestio would be highly apriciated.> > >