From owner-chemistry@ccl.net Fri Jul 30 00:48:00 2010 From: "Heng Zhang chemzhh..163.com" To: CCL Subject: CCL:G: how to choose basis set for optimization of organic molecular Message-Id: <-42385-100729212749-21949-RXas2LdUfOhuJ7NBQRbQog=-=server.ccl.net> X-Original-From: "Heng Zhang" Date: Thu, 29 Jul 2010 21:27:47 -0400 Sent to CCL by: "Heng Zhang" [chemzhh,,163.com] Hi, everyone I am optimizing a molecular C8H8ClNO. There may be two isomers whose energy is very close (less than 0.45 kcal/mol by using 6-31+g*). I want to compute the accurate structure and energy of this molecular by using high precision basis set. Can any one give some suggestions? Thanks. By the way, in that kind of calculation using Gaussian, is there some other things that should be paied attention to. Heng Zhang From owner-chemistry@ccl.net Fri Jul 30 05:20:00 2010 From: "Herbert Fruchtl herbert.fruchtl],[st-andrews.ac.uk" To: CCL Subject: CCL:G: how to choose basis set for optimization of organic molecular Message-Id: <-42386-100730051436-6068-beJZc+Pasg1+Vp2shwhUaQ::server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Jul 2010 10:14:20 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl ~~ st-andrews.ac.uk] If you want a series of basis sets with systematic convergence to the CBS (complete basis set) limit, look at the Dunning basis sets (cc-pvdz, cc-pvtz, etc.). For a single small molecule you probably don't need extra diffuse basis sets (aug-cc-pvNz, or "+" with Pople basis sets). What is probabbly even more important is the method. If you use DFT, go for one of the more modern meta-hybrid functionals (e.g. M06-2X). The best "black box" ab initio method for molecules of this size would be CCSD(T), but a geometry optimization with that can get expensive. Gaussian might not be the most appropriate program in that case. HTH, Herbert Heng Zhang chemzhh..163.com wrote: > Sent to CCL by: "Heng Zhang" [chemzhh,,163.com] > Hi, everyone > I am optimizing a molecular C8H8ClNO. There may be two isomers whose energy is very close (less than 0.45 kcal/mol by using 6-31+g*). I want to compute the accurate structure and energy of this molecular by using high precision basis set. Can any one give some suggestions? Thanks. > By the way, in that kind of calculation using Gaussian, is there some other things that should be paied attention to. > > Heng Zhang> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Jul 30 05:54:00 2010 From: "Gadzikano Munyuki gadzie===gmail.com" To: CCL Subject: CCL:G: Gaussian09 Error Message-Id: <-42387-100730053047-14028-seeIlcL0liXAWLhiawBCTg%server.ccl.net> X-Original-From: Gadzikano Munyuki Content-Type: multipart/alternative; boundary=005045029bef2d35ec048c9781c0 Date: Fri, 30 Jul 2010 11:30:41 +0200 MIME-Version: 1.0 Sent to CCL by: Gadzikano Munyuki [gadzie],[gmail.com] --005045029bef2d35ec048c9781c0 Content-Type: text/plain; charset=ISO-8859-1 Hi Jamin and Robert I did what you are suggesting before and i was getting the same error... that was the input file i used. %NProcShared=8 %nprocl=8 %chk=start1.chk %mem=128mw # b3lyp/3-21G freq geom=allcheck guess=read --Link1-- %NProcShared=8 %nprocl=8 %chk=start1.chk %mem=128mw #n b3lyp/6-31G opt=readfc geom=allcheck scf=(qc,maxcycle=1000) On Thu, Jul 29, 2010 at 10:57 PM, Jamin Krinsky jamink-,-berkeley.edu < owner-chemistry+*+ccl.net> wrote: > Gadzikano, Robert, > > It is hard for me to tell whether it is a memory or disk space error, but > the job is definitely running out of resources during the calculation of > force constants. Robert is right that you normally don't need to calculate > forces at the beginning of a geometry optimization (the opt=calcfc keyword), > however you will need to do a frequency calculation at the end (which will > fail similarly with the resources you are allocating). The suggestion of > doing the frequencies using a smaller basis is not sound: a vibrational > analysis on a structure optimized at a different level of theory is > meaningless, because the stationary point will be located at different > places in coordinate space for different methods (in this case basis set > size). > > Regards, > Jamin > > > > On Thu, Jul 29, 2010 at 12:09 PM, Robert McGibbon rmcgibbo[A]princeton.edu > wrote: > >> Gadzikano, >> >> I'm not entirely sure what your problem is, as I've never seen that error. >> However, I would not recommend using the 'opt=calcfc' keyword. Computing the >> force constants at the beginning is very costly and could be where your >> error is coming. It might be preferable to use the force constants from a >> freq job with the 3-21G basis set as the initial guess Hessian instead - >> this can be done with the opt=readfckeyword. >> >> Just my $0.02, >> -robert >> >> >> On Thu, Jul 29, 2010 at 4:40 AM, Gadzikano Munyuki gadzie(!)gmail.com < >> owner-chemistry.:.ccl.net> wrote: >> >>> Hi all, >>> >>> I am trying to do an optimization job of a calcium-peptide complex using >>> gaussian09. the peptide is quite big, it has 10 residues . I managed to >>> optimize the structure without any problems with a smaller basis set 3-21G. >>> However when i try to adopt a bigger basis set i am getting the error below >>> >>> Any help will be very appreciated.... >>> >>> >>> ----------------------------- >>> -------------- >>> # b3lyp/6-31G Opt=calcfc geom=allcheck guess=read >>> scf=(qc,maxcycle=1000) >>> >>> >>> ------------------------------------------- >>> 1/10=4,29=7,30=1,38=1/1,3; >>> 2/12=2,40=1/2; >>> 3/5=5,11=2,14=-4,16=1,25=1,30=1,71=2,74=-5,116=-2/1,2,3; >>> 4/5=1/1; >>> 5/5=2,38=6,98=1/2; >>> 8/6=4,10=90,11=11/1; >>> 11/6=1,8=1,9=11,15=111,16=1/1,2,10; >>> 10/6=1/2; >>> 6/7=2,8=2,9=2,10=2,18=1,28=1/1; >>> 7/8=1,10=1,25=1/1,2,3,16; >>> 1/10=4,30=1/3; >>> >>> >>> ............................................................ >>> >>> Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. >>> FoFDir/FoFCou used for L=0 through L=1. >>> End of G2Drv Frequency-dependent properties file 721 does not exist. >>> End of G2Drv Frequency-dependent properties file 722 does not exist. >>> IDoAtm=11111111111111111111111111111111111111111111111111 >>> IDoAtm=11111111111111111111111111111111111111111111111111 >>> IDoAtm=11111111111111111111111111111111111111111111111111 >>> IDoAtm=11111111111111111111111111111111111111111111 >>> Differentiating once with respect to electric field. >>> with respect to dipole field. >>> Differentiating once with respect to nuclear coordinates. >>> There are 585 degrees of freedom in the 1st order CPHF. >>> IDoFFX=5. >>> 585 vectors produced by pass 0 Test12= 2.74D-13 1.00D-09 XBig12= >>> 1.01D+05 2.93D+02. >>> AX will form 18 AO Fock derivatives at one time. >>> 585 vectors produced by pass 1 Test12= 2.74D-13 1.00D-09 XBig12= >>> 1.16D+04 1.47D+01. >>> 585 vectors produced by pass 2 Test12= 2.74D-13 1.00D-09 XBig12= >>> 4.64D+01 5.44D-01. >>> 582 vectors produced by pass 3 Test12= 2.74D-13 1.00D-09 XBig12= >>> 1.01D-01 1.97D-02. >>> 582 vectors produced by pass 4 Test12= 2.74D-13 1.00D-09 XBig12= >>> 1.18D-04 4.58D-04. >>> 327 vectors produced by pass 5 Test12= 2.74D-13 1.00D-09 XBig12= >>> 9.50D-08 1.64D-05. >>> 16 vectors produced by pass 6 Test12= 2.74D-13 1.00D-09 XBig12= >>> 6.51D-11 3.18D-07. >>> 3 vectors produced by pass 7 Test12= 2.74D-13 1.00D-09 XBig12= >>> 4.67D-14 7.29D-09. >>> Inverted reduced A of dimension 3265 with in-core refinement. >>> NIJ > Max2 in MMCore. >>> Error termination via Lnk1e in >>> /opt/gridware/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010. >>> Job cpu time: 1 days 23 hours 4 minutes 27.7 seconds. >>> File lengths (MBytes): RWF= 31540 Int= 0 D2E= 0 Chk= 96 >>> Scr= 1 >>> failed to open execfile >>> >> >> > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink,berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > --005045029bef2d35ec048c9781c0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Jamin and Robert

I did what you are suggesting before and i was = getting the same error... that was the input file i used.

%NProcShar= ed=3D8
=A0%nprocl=3D8
=A0%chk=3Dstart1.chk
=A0%mem=3D128mw
=A0#= b3lyp/3-21G freq geom=3Dallcheck guess=3Dread

--Link1--
%NProcShared=3D8
=A0%nprocl=3D8
=A0%chk=3Dstart1.chk
=A0%mem=3D128mw
#n b3lyp/6-31G opt=3Dreadfc geom=3Dallcheck scf=3D(qc,ma= xcycle=3D1000)


On Thu, Jul 29, 2010 a= t 10:57 PM, Jamin Krinsky jamink-,-berkeley= .edu <o= wner-chemistry+*+ccl.net> wrote:
Gadzikano, Robert= ,

It is hard for me to tell whether it is a memory or disk space err= or, but the job is definitely running out of resources during the calculati= on of force constants. Robert is right that you normally don't need to = calculate forces at the beginning of a geometry optimization (the opt=3Dcal= cfc keyword), however you will need to do a frequency calculation at the en= d (which will fail similarly with the resources you are allocating). The su= ggestion of doing the frequencies using a smaller basis is not sound: a vib= rational analysis on a structure optimized at a different level of theory i= s meaningless, because the stationary point will be located at different pl= aces in coordinate space for different methods (in this case basis set size= ).

Regards,
Jamin



On Thu, Jul 29, 2010 at 12:09 PM, Robert McGibbon rmcgib= bo[A]princeton.edu <= span dir=3D"ltr"><owner-chemistry,ccl.net> wrote:
Gadzikano,

I'm not entirely sure what your problem is, as I'= ;ve never seen that error. However, I would not recommend using the 'op= t=3Dcalcfc' keyword. Computing the force constants at the beginning is = very costly and could be where your error is coming. It might be preferable= to use the force constants from a freq job with the 3-21G basis set as the= initial guess Hessian instead - this can be done with the opt=3Dreadfc keyword.

Just my $0.02,
-robert


On Thu, Jul 29, 2010 at 4:40 AM, Gadz= ikano Munyuki gadzie(!)gmail= .com <owner-chemistry.:.ccl.net> wrote:
Hi all,

I = am trying to do an optimization job of a calcium-peptide complex using gaussian09. the peptide is quite big, it=A0 has 10 residues=A0 . I managed to optimize the structure without any problems with a smaller basis set 3-21G. However when i try to adopt a bigger basis set i am getting the error below

Any help will be very appreciated....


=A0-------------------= ----------
--------------
=A0# b3lyp/6-31G=A0 Opt=3Dcalcfc geom=3Dal= lcheck guess=3Dread scf=3D(qc,maxcycle=3D1000)


=A0--------------= -----------------------------
=A01/10=3D4,29=3D7,30=3D1,38=3D1/1,3;
=A02/12=3D2,40=3D1/2;
=A03/5=3D= 5,11=3D2,14=3D-4,16=3D1,25=3D1,30=3D1,71=3D2,74=3D-5,116=3D-2/1,2,3;
=A0= 4/5=3D1/1;
=A05/5=3D2,38=3D6,98=3D1/2;
=A08/6=3D4,10=3D90,11=3D11/1;<= br>=A011/6=3D1,8=3D1,9=3D11,15=3D111,16=3D1/1,2,10;
=A010/6=3D1/2;
=A06/7=3D2,8=3D2,9=3D2,10=3D2,18=3D1,28=3D1/1;
=A07/8=3D1,10=3D1,25=3D1/= 1,2,3,16;
=A01/10=3D4,30=3D1/3;


.............................= ...............................

=A0Calling FoFCou, ICntrl=3D=A0 3107= FMM=3DT I1Cent=3D=A0=A0 0 AccDes=3D 0.00D+00.
=A0FoFDir/FoFCou used for L=3D0 through L=3D1.
=A0End of G2Drv Frequency= -dependent properties file=A0=A0 721 does not exist.
=A0End of G2Drv Fre= quency-dependent properties file=A0=A0 722 does not exist.
=A0=A0=A0=A0= =A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111111111111111=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111= 111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D1111111111111111111111= 1111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D111111= 11111111111111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Diffe= rentiating once with respect to electric field.
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 with respect to dipole field.=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to nuclea= r coordinates.
=A0=A0=A0=A0=A0=A0=A0=A0=A0 There are=A0=A0 585 degrees o= f freedom in the 1st order CPHF.=A0 IDoFFX=3D5.
=A0=A0=A0 585 vectors pr= oduced by pass=A0 0 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.01D+05 2.93D+02= .
=A0AX will form=A0=A0=A0 18 AO Fock derivatives at one time.
=A0=A0=A0 5= 85 vectors produced by pass=A0 1 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.16= D+04 1.47D+01.
=A0=A0=A0 585 vectors produced by pass=A0 2 Test12=3D 2.7= 4D-13 1.00D-09 XBig12=3D 4.64D+01 5.44D-01.
=A0=A0=A0 582 vectors produced by pass=A0 3 Test12=3D 2.74D-13 1.00D-09 XBi= g12=3D 1.01D-01 1.97D-02.
=A0=A0=A0 582 vectors produced by pass=A0 4 Te= st12=3D 2.74D-13 1.00D-09 XBig12=3D 1.18D-04 4.58D-04.
=A0=A0=A0 327 vec= tors produced by pass=A0 5 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 9.50D-08 1= .64D-05.
=A0=A0=A0=A0 16 vectors produced by pass=A0 6 Test12=3D 2.74D-13 1.00D-09 X= Big12=3D 6.51D-11 3.18D-07.
=A0=A0=A0=A0=A0 3 vectors produced by pass= =A0 7 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 4.67D-14 7.29D-09.
=A0Invert= ed reduced A of dimension=A0 3265 with in-core refinement.
=A0NIJ > Max2 in MMCore.
=A0Error termination via Lnk1e in /opt/gridw= are/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010.
=A0Jo= b cpu time:=A0 1 days 23 hours=A0 4 minutes 27.7 seconds.
=A0File length= s (MBytes):=A0 RWF=3D=A0 31540 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0=A0=A0=A0= =A0 0 Chk=3D=A0=A0=A0=A0 96 Scr=3D=A0=A0=A0=A0=A0 1
failed to open execfile




--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation F= acility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink,berkeley.edu<= /a>, 510-643-0616
http://glab.cc= hem.berkeley.edu


--005045029bef2d35ec048c9781c0-- From owner-chemistry@ccl.net Fri Jul 30 07:01:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek^^few.vu.nl" To: CCL Subject: CCL: how to choose basis set for optimization of organic molecular Message-Id: <-42388-100730062000-20159-DmSm2DmFg8L7/pIyDkxTOg[-]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Jul 2010 12:19:53 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek-,-few.vu.nl] > Sent to CCL by: "Heng  Zhang" [chemzhh,,163.com] > Hi, everyone > I am optimizing a molecular C8H8ClNO. There may be two isomers whose energy is very close (less than 0.45 kcal/mol by using 6-31+g*). I want to compute the accurate structure and energy of this molecular by using high precision basis set. Can any one give some suggestions? Thanks. There is no dft method that I am aware of that is accurate to 0.45 kcal/mol, and at this level you should also include dispersion and vibrational effects (and thermodynamics!). This talk by T. Helgaker gives a good overview of the basis set and correlation effects: http://folk.uio.no/helgaker/talks/esor.pdf Of course just because you might not be able to say which of the two isomers have the lowest energy doesn't mean that your structures will be inaccurate, they may well be ok with standard dft methods, specially if your molecule is not too floppy. Use a triple-zeta basis set in the final stages of your geometry optimization. Sincerely, Ulf Ekström From owner-chemistry@ccl.net Fri Jul 30 08:16:01 2010 From: "Marcel Swart marcel.swart/./udg.edu" To: CCL Subject: CCL: Density Functionals 2010 Message-Id: <-42389-100730031034-19261-CYMHQOJp8NpWdETGKn1ipg]=[server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-6--628568963 Date: Fri, 30 Jul 2010 09:10:25 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Marcel Swart [marcel.swart::udg.edu] --Apple-Mail-6--628568963 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 We have recently hosted the IXth Girona Seminar = (http://iqc.udg.edu/gs2010/), which had Density Functional Theory as one of the topics. One of the = things that came up was the popularity of current density functionals, and how = these could be used to generate a "consensus" DFT method by taking a linear combination of a number of popular DFT methods. This "consensus" method will probably be more accurate than the GFSRPM method that was also revealed during the conference, and therefore we have setup a popularity poll for density functional methods for the year 2010. The number of density functionals is limited by choice to 20, with 5-10 = places reserved for additional suggestions; in future editions this may be = extended. Please add your choice for the best (and worst) density functional at: http://bit.ly/cQPX2w The poll is open until Oct. 1 after which a ranking will be made. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart-$-icrea.es marcel.swart-$-udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-6--628568963 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 http://iqc.udg.edu/gs2010/),=
which had Density Functional Theory as one of the topics. One of = the things
that came up was the popularity of current density = functionals, and how these
could be used to generate a = "consensus" DFT method by taking a linear
combination of a = number of popular DFT methods.

This = "consensus" method will probably be more accurate = than
the GFSRPM method that was also revealed during the = conference,
and therefore we have setup a popularity poll for = density functional
methods for the year = 2010.

The number of density functionals is = limited by choice to 20, with 5-10 places
reserved for = additional suggestions; in future editions this may be = extended.
Please add your choice for the best (and worst) = density functional at:

http://bit.ly/cQPX2w

The poll is open until = Oct. 1 after which a ranking will be made.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Institut de Qu=EDmica = Computacional
Universitat de Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
Pic de Peguera 15
17003 Girona

+34-972-183240
fax
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= --Apple-Mail-6--628568963-- From owner-chemistry@ccl.net Fri Jul 30 08:51:01 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis-.-borealisgroup.com" To: CCL Subject: CCL:G: NewZmat Conversion Problem Message-Id: <-42390-100730051742-8117-NjblqZL+k7zjQU36+ZF/sA[#]server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2BD27C21A5B53C4AB53F403FC915A1820145C9D971CMS02mignetwo_" Date: Fri, 30 Jul 2010 11:17:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis*_*borealisgroup.com] --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9D971CMS02mignetwo_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thanks for the suggestions=0D=0A=0D=0AI will try using a third party progra= m for the conversion and see how far I get=2E=0D=0A=0D=0AAgain thanks a lot= =2E You've been more than helpful and I truly appreciate it=0D=0A=0D=0AThom= as=0D=0A=0D=0AFrom: owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup= =2Ecom*_*ccl=2Enet [mailto:owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgr= oup=2Ecom*_*ccl=2Enet] On Behalf Of Mahmoud A=2E A=2E Ibrahim m=2Eibrahim(0)c= ompchem=2Enet=0D=0ASent: Thursday, July 29, 2010 3:20 AM=0D=0ATo: Gkourmpis= , Thomas=0D=0ASubject: CCL:G: NewZmat Conversion Problem=0D=0A=0D=0ADear Th= omas=0D=0AI don't use windows version, but I have tested the NewZmat option= , and it works well=2E=0D=0AAs I told you I am not expert with Windows vers= ion, but I have some idea:=0D=0A* have you tried to use NewZmat utility in = linux version=2E=0D=0A* you can generate the optimized structures from you= r output and there are a lot of programs can be used to extract the structu= res from the output (like; Chemcraft), and then you can use OpenBabel to co= nvert the file to the desired file format=2E=0D=0A* GaussView reads the fin= al optimized structure from the checkpoint file=2E=0D=0AMay be I am missing= something here, and hope somebody else able to help you=2E=0D=0Asincerely;= =0D=0AM=2E Ibrahim=0D=0A=0D=0A=0D=0A=0D=0AOn Wed, Jul 28, 2010 at 9:01 AM, = Thomas Gkourmpis thomas=2Egkourmpis{}borealisgroup=2Ecom >= wrote:=0D=0A=0D=0ASent to CCL by: "Thomas Gkourmpis" [thomas=2Egkourmpis~= !~borealisgroup=2Ecom]=0D=0AHello everyone=0D= =0A=0D=0AI seem to have a problem in using the NewZmat Conversion routine i= n Gaussian03W, and I really don't understand what I am doing wrong (somethi= ng obviously, but I can't really get it)=2E=0D=0A=0D=0AI am trying to conve= rt a checkpoint file to gjf and pdb files for usage in the ChemRate program= to calculate the reaction rate parameters of a particular reaction=2E=0D= =0A=0D=0AI go to the Utilities Tab in Gaussian, chose NewZmat and I am just= pressing the convert button to convert the file in question to the format = I need (chosen from the Options Menu)=2E There I get a message on the Gauss= ian window that the processing is complete but nothing actually happens=2E = No converted file can be found on the appropriate directory (in any directo= ry actually I did search them all) and no error message=2E=0D=0A=0D=0AI am = at loss here=2E Any ideas or suggestions on what I am doing wrong? (this is= the first time I am using NewZmat)=0D=0A=0D=0AThanks in advance=0D=0A=0D= =0AThomas=0D=0A=0D=0A=0D=0A=0D=0A-=3D This is automatically added to each m= essage by the mailing script =3D- or use:=0D=0A htt= p://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message=0D=0A=0D=0AE-mail to admin= istrators: CHEMISTRY-REQUEST[a]ccl=2Enet or use=0D=0A http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message=0D= =0A=0D=0ASubscribe/Unsubscribe:=0D=0A http://www=2Eccl=2Enet/chemistry/= sub_unsub=2Eshtml=0D=0A=0D=0ABefore posting, check wait time at: http://www= =2Eccl=2Enet=0D=0A=0D=0AJob: http://www=2Eccl=2Enet/jobs=0D=0AConferences: = http://server=2Eccl=2Enet/chemistry/announcements/conferences/=0D=0A=0D=0AS= earch Messages: http://www=2Eccl=2Enet/chemistry/searchccl/index=2Eshtml=0D= =0A=0D=0A Website: www= =2Ecompchem=2Enet=0D=0A Fax = No=2E: +20862342601=0D=0A=0D=0A=0D=0A --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9D971CMS02mignetwo_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable =0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A

Thanks= for the suggestions

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=  

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<= span style=3D'font-size:10=2E0pt;font-family:"Arial","sans-serif";=0D=0Acol= or:#1F497D'>I will try using a third party program for the conversion and= =0D=0Asee how far I get=2E

=0D=0A=0D=0A

 

=0D=0A=0D=0A

Again thanks a lot=2E You’ve been more than help= ful and I truly=0D=0Aappreciate it

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=0D=0A=0D=0A

Thomas

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From:=0D=0Aowner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom*_*cc= l=2Enet=0D=0A[mailto:owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup= =2Ecom*_*ccl=2Enet] On=0D=0ABehalf Of Mahmoud A=2E A=2E Ibrahim m=2Eib= rahim(0)compchem=2Enet
=0D=0ASent: Thursday, July 29, 2010 3:20 A= M
=0D=0ATo: Gkourmpis, Thomas
=0D=0ASubject: CCL:G: New= Zmat Conversion Problem

=0D=0A=0D=0A
=0D=0A=0D=0A=

 

=0D=0A=0D=0A

= Dear Thomas

=0D=0A=0D=0A
=0D=0A=0D=0A

I don't use windows version, but I have tested the NewZmat=0D=0Aoption, an= d it works well=2E

=0D=0A=0D=0A
=0D=0A=0D=0A
=0D=0A= =0D=0A

As I told you I am not expert with Windows versi= on, but I=0D=0Ahave some idea:

=0D=0A=0D=0A
=0D=0A=0D=0A=
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* have you tried to use NewZmat utili= ty in linux version=2E

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*  you can generate the optimized struct= ures from your=0D=0Aoutput and there are a lot of programs can be used to e= xtract the structures=0D=0Afrom the output (like; Chemcraft), and then you = can use OpenBabel to convert=0D=0Athe file to the desired file format=2E

=0D=0A=0D=0A
=0D=0A=0D=0A
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* GaussView reads the final optimized structure from the=0D=0Acheckpoi= nt file=2E 

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May be I am missing something here, and hope somebo= dy else=0D=0Aable to help you=2E

=0D=0A=0D=0A
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=0D=0A=0D=0A

sincerely;

=0D=0A=0D= =0A
=0D=0A=0D=0A
=0D=0A=0D=0A

M=2E Ibrahim

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On Wed, Jul 28, 2010 at 9:01 AM, Thomas Gkour= mpis=0D=0Athomas=2Egkourmpis{}boreal= isgroup=2Ecom <o= wner-chemistry[a]ccl=2Enet>=0D=0Awrote:

=0D=0A=0D=0A
=0D=0ASent to CCL b= y: "Thomas  Gkourmpis" [thomas=2Egkourmpis~!~borealisgroup=2Ecom]
= =0D=0AHello everyone
=0D=0A
=0D=0AI seem to have a problem in using t= he NewZmat Conversion routine in=0D=0AGaussian03W, and I really don't under= stand what I am doing wrong (something=0D=0Aobviously, but I can't really g= et it)=2E
=0D=0A
=0D=0AI am trying to convert a checkpoint file to gj= f and pdb files for usage in the=0D=0AChemRate program to calculate the rea= ction rate parameters of a particular=0D=0Areaction=2E
=0D=0A
=0D=0AI= go to the Utilities Tab in Gaussian, chose NewZmat and I am just pressing = the=0D=0Aconvert button to convert the file in question to the format I nee= d (chosen=0D=0Afrom the Options Menu)=2E There I get a message on the Gauss= ian window that the=0D=0Aprocessing is complete but nothing actually happen= s=2E No converted file can be=0D=0Afound on the appropriate directory (in a= ny directory actually I did search them=0D=0Aall) and no error message=2E=0D=0A
=0D=0AI am at loss here=2E Any ideas or suggestions on what I a= m doing wrong? (this is=0D=0Athe first time I am using NewZmat)
=0D=0A=0D=0AThanks in advance
=0D=0A
=0D=0AThomas
=0D=0A
=0D=0A
= =0D=0A
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=0D=0A
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= =0D=0A                  Mahmou= d A=2E A=2E=0D=0AIbrahim        
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=0D=0A=0D=0A<= /div>=0D=0A=0D=0A
=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9D971CMS02mignetwo_-- From owner-chemistry@ccl.net Fri Jul 30 09:25:00 2010 From: "Alberto Sergio Garay sgaray===fbcb.unl.edu.ar" To: CCL Subject: CCL: Request for Deuterium Order parameters of ETHER LIPIDS.. Message-Id: <-42391-100730082017-7626-aweAOphyO5j3RI+wHstGfA{=}server.ccl.net> X-Original-From: Alberto Sergio Garay Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 30 Jul 2010 09:20:08 -0300 MIME-Version: 1.0 Sent to CCL by: Alberto Sergio Garay [sgaray^^^fbcb.unl.edu.ar] Dear all I'm looking for Deuterium Order parameters of Ether lipids' tails but without success. I need it in order to test some of my Molecular Dynamics simulations of DHPC (Dihexadecyl-Phosphatidylcholine). Please, if someone know about some papers (or experimental values not published) where some of this parameters are shown, I would very appreciate this help. Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 From owner-chemistry@ccl.net Fri Jul 30 13:37:00 2010 From: "Jamin Krinsky jamink[-]berkeley.edu" To: CCL Subject: CCL:G: Gaussian09 Error Message-Id: <-42392-100730132419-14745-E5Vc75m/92Y/cG2LnWzvaA()server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 30 Jul 2010 10:24:09 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[]berkeley.edu] Gadzikano, Before you said the frequency calculation worked with the small basis set. Now it is dying in the first part of your job (before the Link1)? Also, neither of us were suggesting that you do frequencies using a small basis set and then optimize again with a larger one, which is what your input is doing. To be clear, you are specifying that the job be run on 8 processors each on 8 nodes, for a total of 64 processors. Your are only specifying 128 MW of memory per 8 processors. Is that all the RAM available on each node? If there is more you should use it. Unless there is something strange about about your system (tiny disks, etc.) you should be able to run a frequency calculation on a 150-atom peptide using 6-31G(d) without a problem. Your issue MAY be a network problem with LINDA related to your two-part job. I would suggest doing the following two separate calculations, meaning run the first one, and when it finishes submit the second one using the optimized geometry. Job #1 %NProcShared=8 %nprocl=8 %chk=start1.chk %mem=128mw # b3lyp/6-31G(d) opt title Molec. Spec. Now copy start1.chk to start2.chk Job #2 %NProcShared=8 %nprocl=8 %chk=start2.chk %mem=(Specify the maximum amount of memory your can, per node of 8 processors) # b3lyp/6-31G(d) freq geom=allcheck guess=read In addition to diagnosing possible LINDA issues, this could get around some problems with memory allocation that Gaussian has with multi-step jobs. Jamin On Fri, Jul 30, 2010 at 2:30 AM, Gadzikano Munyuki gadzie===gmail.com wrote: > Hi Jamin and Robert > > I did what you are suggesting before and i was getting the same error... > that was the input file i used. > > %NProcShared=8 >  %nprocl=8 >  %chk=start1.chk >  %mem=128mw >  # b3lyp/3-21G freq geom=allcheck guess=read > > --Link1-- > %NProcShared=8 >  %nprocl=8 >  %chk=start1.chk >  %mem=128mw > #n b3lyp/6-31G opt=readfc geom=allcheck scf=(qc,maxcycle=1000) > > > On Thu, Jul 29, 2010 at 10:57 PM, Jamin Krinsky jamink-,-berkeley.edu > wrote: >> >> Gadzikano, Robert, >> >> It is hard for me to tell whether it is a memory or disk space error, but >> the job is definitely running out of resources during the calculation of >> force constants. Robert is right that you normally don't need to calculate >> forces at the beginning of a geometry optimization (the opt=calcfc keyword), >> however you will need to do a frequency calculation at the end (which will >> fail similarly with the resources you are allocating). The suggestion of >> doing the frequencies using a smaller basis is not sound: a vibrational >> analysis on a structure optimized at a different level of theory is >> meaningless, because the stationary point will be located at different >> places in coordinate space for different methods (in this case basis set >> size). >> >> Regards, >> Jamin >> >> >> On Thu, Jul 29, 2010 at 12:09 PM, Robert McGibbon rmcgibbo[A]princeton.edu >> wrote: >>> >>> Gadzikano, >>> I'm not entirely sure what your problem is, as I've never seen that >>> error. However, I would not recommend using the 'opt=calcfc' keyword. >>> Computing the force constants at the beginning is very costly and could be >>> where your error is coming. It might be preferable to use the force >>> constants from a freq job with the 3-21G basis set as the initial guess >>> Hessian instead - this can be done with the opt=readfc keyword. >>> Just my $0.02, >>> -robert >>> >>> On Thu, Jul 29, 2010 at 4:40 AM, Gadzikano Munyuki gadzie(!)gmail.com >>> wrote: >>>> >>>> Hi all, >>>> >>>> I am trying to do an optimization job of a calcium-peptide complex using >>>> gaussian09. the peptide is quite big, it  has 10 residues  . I managed to >>>> optimize the structure without any problems with a smaller basis set 3-21G. >>>> However when i try to adopt a bigger basis set i am getting the error below >>>> >>>> Any help will be very appreciated.... >>>> >>>> >>>>  ----------------------------- >>>> -------------- >>>>  # b3lyp/6-31G  Opt=calcfc geom=allcheck guess=read >>>> scf=(qc,maxcycle=1000) >>>> >>>> >>>>  ------------------------------------------- >>>>  1/10=4,29=7,30=1,38=1/1,3; >>>>  2/12=2,40=1/2; >>>>  3/5=5,11=2,14=-4,16=1,25=1,30=1,71=2,74=-5,116=-2/1,2,3; >>>>  4/5=1/1; >>>>  5/5=2,38=6,98=1/2; >>>>  8/6=4,10=90,11=11/1; >>>>  11/6=1,8=1,9=11,15=111,16=1/1,2,10; >>>>  10/6=1/2; >>>>  6/7=2,8=2,9=2,10=2,18=1,28=1/1; >>>>  7/8=1,10=1,25=1/1,2,3,16; >>>>  1/10=4,30=1/3; >>>> >>>> >>>> ............................................................ >>>> >>>>  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >>>>  FoFDir/FoFCou used for L=0 through L=1. >>>>  End of G2Drv Frequency-dependent properties file   721 does not exist. >>>>  End of G2Drv Frequency-dependent properties file   722 does not exist. >>>>           IDoAtm=11111111111111111111111111111111111111111111111111 >>>>           IDoAtm=11111111111111111111111111111111111111111111111111 >>>>           IDoAtm=11111111111111111111111111111111111111111111111111 >>>>           IDoAtm=11111111111111111111111111111111111111111111 >>>>           Differentiating once with respect to electric field. >>>>                 with respect to dipole field. >>>>           Differentiating once with respect to nuclear coordinates. >>>>           There are   585 degrees of freedom in the 1st order CPHF. >>>> IDoFFX=5. >>>>     585 vectors produced by pass  0 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 1.01D+05 2.93D+02. >>>>  AX will form    18 AO Fock derivatives at one time. >>>>     585 vectors produced by pass  1 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 1.16D+04 1.47D+01. >>>>     585 vectors produced by pass  2 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 4.64D+01 5.44D-01. >>>>     582 vectors produced by pass  3 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 1.01D-01 1.97D-02. >>>>     582 vectors produced by pass  4 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 1.18D-04 4.58D-04. >>>>     327 vectors produced by pass  5 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 9.50D-08 1.64D-05. >>>>      16 vectors produced by pass  6 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 6.51D-11 3.18D-07. >>>>       3 vectors produced by pass  7 Test12= 2.74D-13 1.00D-09 XBig12= >>>> 4.67D-14 7.29D-09. >>>>  Inverted reduced A of dimension  3265 with in-core refinement. >>>>  NIJ > Max2 in MMCore. >>>>  Error termination via Lnk1e in >>>> /opt/gridware/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010. >>>>  Job cpu time:  1 days 23 hours  4 minutes 27.7 seconds. >>>>  File lengths (MBytes):  RWF=  31540 Int=      0 D2E=      0 Chk=     96 >>>> Scr=      1 >>>> failed to open execfile >> >> >> >> -- >> Jamin L Krinsky, Ph.D. >> Molecular Graphics and Computation Facility >> 175 Tan Hall, University of California, Berkeley, CA 94720 >> jamink,berkeley.edu, 510-643-0616 >> http://glab.cchem.berkeley.edu >> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink*o*berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Fri Jul 30 17:31:00 2010 From: "David Hoover hooverdm||helix.nih.gov" To: CCL Subject: CCL:G: unknown Gaussian09 error Message-Id: <-42393-100730161009-2100-OTHfpc18JIMSvql3MpGjaw%server.ccl.net> X-Original-From: David Hoover Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Jul 2010 16:10:02 -0400 MIME-Version: 1.0 Sent to CCL by: David Hoover [hooverdm- -helix.nih.gov] Would anyone be able to interpret the following error from Gaussian09? Error: segmentation violation, address not mapped to object rax 00002aa8ae47f150, rbx 000000000001e0b4, rcx 00002aab69413790 rdx 0000000000000043, rsp 000000005428c1c0, rbp 000000005428c2f0 rsi 0000000000000016, rdi 00000000000000fd, r8 000000000000137c r9 00000000014e2338, r10 0000000000000000, r11 00000000000008b9 r12 0000000000048783, r13 0000000000000001, r14 000000005428e610 r15 0000000000000387 0 0xb1a5c0 pickr4_ + 0x270 1 0x802659 prmraf_ + 0x4ca9 2 0x5bef3a prrfsu_ + 0x31ba 3 0x520f3e fofraf_ + 0x1b2e 4 0x5107b0 fofdir_ + 0x2750 5 0x4fbe95 fof2e_ + 0x1485 6 0x4c2330 axfrmf_ + 0xd90 7 0x66c722 ax_ + 0x1012 8 0x552ee2 lineq2_ + 0xe52 9 0x4d662b cphf_ + 0x1f2b 10 0x40e22e minotr_ + 0xaafe 11 0x403710 MAIN_ + 0xb0 12 0x403648 ********************************************************************* David Hoover Helix Systems Staff http://helix.nih.gov From owner-chemistry@ccl.net Fri Jul 30 20:39:00 2010 From: "David Mannock dmannock|,|ualberta.ca" To: CCL Subject: CCL: Request for Deuterium Order parameters of ETHER LIPIDS.. Message-Id: <-42394-100730203734-19319-dhAt6IgAI0wdF+GEnmc81Q]~[server.ccl.net> X-Original-From: David Mannock Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Jul 2010 18:37:22 -0600 MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock-.-ualberta.ca] Sergio, Look at some of Harold Jarrell's papers in the 1980s. He did a lot of glycolipid 2H-NMR, but will have cited PL work. You should be able to trace the references back and forward through their citations. David Mannock On 7/30/2010 6:20 AM, Alberto Sergio Garay sgaray===fbcb.unl.edu.ar wrote: > > Sent to CCL by: Alberto Sergio Garay [sgaray^^^fbcb.unl.edu.ar] > Dear all > > I'm looking for Deuterium Order parameters of Ether lipids' tails but > without success. I need it in order to test some of my Molecular > Dynamics simulations of DHPC (Dihexadecyl-Phosphatidylcholine). > > Please, if someone know about some papers (or experimental values not > published) where some of this parameters are shown, I would very > appreciate this help. > > Sergio >