From owner-chemistry@ccl.net Fri May 2 03:09:00 2008 From: "Ulrich Scharfenort scharfenort---ltt.rwth-aachen.de" To: CCL Subject: CCL:G: G problem in freq. calculation Message-Id: <-36878-080502030726-1167-q+o8NKv53paIVUQr6L9F/g{=}server.ccl.net> X-Original-From: Ulrich Scharfenort Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 02 May 2008 09:07:13 +0200 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort_-_ltt.rwth-aachen.de] Hello Raja, normally Gaussian just crashes. It give at least an error code or something out. So I would guess it's not Gaussian but the computer. I get such output when I calculate longer than the time limit of the computer cluster where I calculate. Maybe there is a time limit in the system you are using. Best Wishes Ulrich Scharfenort Raja S r.subramanian(a)ipc.uni-stuttgart.de schrieb: > Sent to CCL by: "Raja S" [r.subramanian- -ipc.uni-stuttgart.de] > Hallo all, > i am calculating vibrational frequencies using freq keyword on a transition metal complex of 100 atoms (6 types of atoms) using b3lyp theory. I use cc-pvdz basis sets for 5 atoms and for the transition metal (Fe) i use SDD basis set. > But the calculation aborts!!! after 3 days. > I submited this job for 300 CPU hrs, 16GB work file size and 1000MW memory in input file. > Can anyone advice me!!! > > the last few lines are as follows:- > DoAtom=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 > NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. > Symmetry not used in FoFCou. > FMM levels: 10 Number of levels for PrismC: 9 > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > There are 135 degrees of freedom in the 1st order CPHF. > 135 vectors were produced by pass 0. > AX will form 135 AO Fock derivatives at one time. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > 135 vectors were produced by pass 1. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > 135 vectors were produced by pass 2. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > 135 vectors were produced by pass 3. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > PrismC: NFx= 2048 NFxT= 6 NFxU= 6. > 135 vectors were produced by pass 4. > > Thanks, > raja.> > > > From owner-chemistry@ccl.net Fri May 2 05:35:01 2008 From: "Rajagopalan S. r.subramanian]*[ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: G problem in freq. calculation Message-Id: <-36879-080502042812-12352-A1V0LDS90VlU5goCAQdmbg[*]server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 02 May 2008 10:27:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian=-=ipc.uni-stuttgart.de] Hello Ulrich and Patrik, Yes I think its the calculation time limit problem (but here max time one can set is 350 hrs!, if i set 300 calculation stops after 3 or 4 days.. )...btw As mr. patrik suggested me to include NoFMM for freq. calculation...i already submitted my job by nofmm.. But the geometry is optimized without NoFMM keywork....is that okay... thanks raja Ulrich Scharfenort scharfenort---ltt.rwth-aachen.de wrote: > > Sent to CCL by: Ulrich Scharfenort [scharfenort_-_ltt.rwth-aachen.de] > Hello Raja, > > normally Gaussian just crashes. It give at least an error code or > something out. > So I would guess it's not Gaussian but the computer. > I get such output when I calculate longer than the time limit of the > computer cluster where I calculate. Maybe there is a time limit in the > system you are using. > > Best Wishes > > Ulrich Scharfenort > > > Raja S r.subramanian(a)ipc.uni-stuttgart.de schrieb: >> Sent to CCL by: "Raja S" [r.subramanian- -ipc.uni-stuttgart.de] >> Hallo all, >> i am calculating vibrational frequencies using freq keyword on a >> transition metal complex of 100 atoms (6 types of atoms) using b3lyp >> theory. I use cc-pvdz basis sets for 5 atoms and for the transition >> metal (Fe) i use SDD basis set. >> But the calculation aborts!!! after 3 days. >> I submited this job for 300 CPU hrs, 16GB work file size and 1000MW >> memory in input file. >> Can anyone advice me!!! >> >> the last few lines are as follows:- >> DoAtom=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT >> Differentiating once with respect to electric field. >> with respect to dipole field. >> Differentiating once with respect to nuclear coordinates. >> FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= >> 8193 >> NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. >> Symmetry not used in FoFCou. >> FMM levels: 10 Number of levels for PrismC: 9 >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> There are 135 degrees of freedom in the 1st order CPHF. >> 135 vectors were produced by pass 0. >> AX will form 135 AO Fock derivatives at one time. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> 135 vectors were produced by pass 1. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> 135 vectors were produced by pass 2. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> 135 vectors were produced by pass 3. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> PrismC: NFx= 2048 NFxT= 6 NFxU= 6. >> 135 vectors were produced by pass 4. >> >> Thanks, >> raja.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- -------------------------------------------------------------------- Rajagopalan Subramanian Institut fuer Physikalische Chemie LS II, Universitaet Stuttgart Pfaffenwaldring 55, D-70569 Stuttgart, Germany EU tel. : +49 711 685 64464, fax : +49 711 685 64443 e-mail: r.subramanian/a\ipc.uni-stuttgart.de -------------------------------------------------------------------- From owner-chemistry@ccl.net Fri May 2 15:37:01 2008 From: "Reaz Uddin riaasuddin[#]yahoo.com" To: CCL Subject: CCL: rmsd problem Message-Id: <-36880-080502143528-15183-j9VzQDQ0EKdLnWp51kBV4w/a\server.ccl.net> X-Original-From: Reaz Uddin Content-Type: text/html; charset=us-ascii Date: Fri, 2 May 2008 10:35:17 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin*o*yahoo.com] 
RMSD.svl in MOE is for calculating rmsds for different conformations of same ligand. It is not for the different ligand. 
GOLD provides an RMSD matrix at the end of log file and you can easily figure out RMSDs between different pairs of conformations/solutions of the same ligand.


REAZUDDIN
Research Scholar
Department of Medicinal Chemistry and Pharmacognosy,
College of Pharmacy, (M/C 781)
University of Illinois at Chicago
833 S. Wood St.
Chicago, IL 60612


--- On Wed, 4/30/08, sobia ahsan halim sobia_halim[a]yahoo.com <owner-chemistry]![ccl.net> wrote:
From: sobia ahsan halim sobia_halim[a]yahoo.com <owner-chemistry]![ccl.net>
Subject: CCL: rmsd problem
To: "UDDIN, REAZ " <riaasuddin]![yahoo.com>
Date: Wednesday, April 30, 2008, 3:49 PM

Sent to CCL by: "sobia ahsan halim" [sobia_halim-x-yahoo.com]
hello all

I am facing problem regarding rmsd. I am calculating the rmsd through MOE 
but when I use structurally different
 compound to measure rmsd against the 
reference molecule (co-crystallized with the protein), it doesn't show any 
rmsd value and give the error that the molecule is structurally not similar. 
And the other thing is how to calculate rmsd on GOLD as GOLD log file 
contain rmsd value but it is the rmsd of the cluster not of different 
conformations of docked ligand. Can any one please tell me how to solve both 
these problems???. Thanks in advance.

With the deepest regards,
Sobia.



Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. From owner-chemistry@ccl.net Fri May 2 19:05:00 2008 From: "Edmanuel Torres e.torres()mpie.de" To: CCL Subject: CCL: Vasp related tools Message-Id: <-36881-080501145013-12604-FJWZI1aTdbEjVGPzaO0pJQ:-:server.ccl.net> X-Original-From: "Edmanuel Torres" Content-Transfer-Encoding: quoted-printable Content-Transfer-Encoding: quoted-printable Content-type: text/plain; charset="utf-8" Content-Type: text/plain; charset="utf-8" Date: Thu, 01 May 2008 20:48:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Edmanuel Torres" [e.torres,+,mpie.de] Hi Kaci=2C You can use AtomEye=2C download the binary from=3A http=3A//mt=2Eseas=2Eupenn=2Eedu/Archive/Graphics/A/ AtomEye analyse distances and other parameters=2C you can use the utility v= asp2cfg to convert from VASP to AtomEye cfg format in a flash=2C http=3A//mt=2Eseas=2Eupenn=2Eedu/Archive/Graphics/A/utils=2Ehtml=23VASP Best=2C Edmanuel ----- Original Message ----- > From=3A Aron Walsh aronjwalsh++gmail=2Ecom =5Bmailto=3Aowner-chemistry=40ccl=2Enet=5D To=3A Torres=2C Edmanuel -id=233in- =5Bmailto=3Ae=2Etorres=40mpie=2Ede=5D Sent=3A Wed=2C 30 Apr 2008 18=3A25=3A10 +0200 Subject=3A CCL=3A Vasp related tools // Hi Kaci=2C //=20 // It sounds like you may have mixed up the coordinate system in your struc= ture // file=2E When you added the molecule check whether the coordinates are // cartesian or fractional=2E By default VASP outputs fractional in CONTCAR= =2C even // when your initial structure =28POSCAR=29 was in cartesian=2E //=20 // VESTA is a very useful =28and free=29 tool for visualizing structures fr= om VASP // and other periodic codes=3A // http=3A//www=2Egeocities=2Ejp/kmo=5Fmma/crystal/en/vesta=2Ehtml //=20 // Good luck! //=20 // Aron //=20 //=20 // On Wed=2C Apr 30=2C 2008 at 7=3A18 AM=2C Kaci Tizi=5FOuzou kaci=2Etiziou= zou*=5F*gmail=2Ecom=3C // owner-chemistry=23=2C=23ccl=2Enet=3E wrote=3A //=20 // =3E Hi folks=2C // =3E // =3E // =3E I have started using Vasp to do a study in heterogenous catalysis=2E= So far=2C // =3E I have figured how to model a crystal =28surface=29=2E // =3E // =3E I am currently stuck since when I put a molecule on top of the surfa= ce=2C // =3E the software does not like it =28complaining distances between atoms= are // =3E small=29=2E // =3E // =3E // =3E =281=29 Question=3A Is there any tool I can use =28before runing Vas= p=29 to check // =3E whether my distances are all right=3F // =3E // =3E =282=29 If someone on this could share with me an input file =28that= works =3A-=29 // =3E that will be great=2E // =3E // =3E // =3E Thanks all // =3E // =3E Cheers // =3E // =3E // =3E Kaci // =3E // =3E //=20= --- Max-Planck-Institut f=C3=BCr Eisenforschung GmbH Max-Planck-Stra=C3=9Fe 1 D-40237 D=C3=BCsseldorf =20 Handelsregister B 2533=20 Amtsgericht D=C3=BCsseldorf =20 Gesch=C3=A4ftsf=C3=BChrung Prof=2E Dr=2E J=C3=B6rg Neugebauer Prof=2E Dr=2E Anke R=2E Pyzalla Prof=2E Dr=2E Dierk Raabe Prof=2E Dr=2E Martin Stratmann Dipl=2E-Kfm=2E Herbert Wilk =20 Ust=2E-Id=2E-Nr=2E=3A DE 11 93 58 514=20 Steuernummer=3A 105 5891 1000 -------------------------------------------------