From owner-chemistry@ccl.net Wed Apr 30 06:51:02 2008 From: "sobia ahsan halim sobia_halim[a]yahoo.com" To: CCL Subject: CCL: rmsd problem Message-Id: <-36865-080430064908-8955-PAiFTbQbxE7pgptpzKsUmw..server.ccl.net> X-Original-From: "sobia ahsan halim" Date: Wed, 30 Apr 2008 06:49:04 -0400 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. From owner-chemistry@ccl.net Wed Apr 30 08:26:00 2008 From: "Trond SAUE tsaue(-)chimie.u-strasbg.fr" To: CCL Subject: CCL: Visualization of NMR shielding tensors Message-Id: <-36866-080430082350-11579-B+QUbkPU0JklfCsL+EQILA[A]server.ccl.net> X-Original-From: "Trond SAUE" Date: Wed, 30 Apr 2008 08:23:46 -0400 Sent to CCL by: "Trond SAUE" [tsaue._+_.chimie.u-strasbg.fr] What software (preferably Linux) allows the visualization of NMR shielding tensors (attached to the molecular structure) ? As far as I know GaussView is capable of this. From owner-chemistry@ccl.net Wed Apr 30 10:03:00 2008 From: "Dominic Ryan dominic.ryan^_^comcast.net" To: CCL Subject: CCL: rmsd problem Message-Id: <-36867-080430095624-11243-4gvpNhMC3YrMNckXJtFaaA|*|server.ccl.net> X-Original-From: Dominic Ryan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 Apr 2008 09:22:59 -0400 MIME-Version: 1.0 Sent to CCL by: Dominic Ryan [dominic.ryan%a%comcast.net] Hello Sobia, Your problem is ill-defined. To calculate an rmsd you have to tell it what atoms to use for the distance measurement. If you use two conformations of the same molecule one can assume that all atoms are to be used, mapping topologically identical atoms. If the molecules are different you will have to decide which ones should be the basis for your comparison. You could consider a scaffold core, or perhaps you have a key set of functional groups that you view as critical, or perhaps you would be interested in a center of mass for a coarser assessment. Dominic Ryan sobia ahsan halim sobia_halim[a]yahoo.com wrote: > 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.> > > > From owner-chemistry@ccl.net Wed Apr 30 10:38:00 2008 From: "Raja S r.subramanian(a)ipc.uni-stuttgart.de" To: CCL Subject: CCL: problem in freq. calculation Message-Id: <-36868-080430100602-13013-16z9kL59zFg39f1oIYvVsg,,server.ccl.net> X-Original-From: "Raja S" Date: Wed, 30 Apr 2008 10:05:58 -0400 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 Wed Apr 30 11:14:00 2008 From: "Andrew Henry ahenry[A]chemcomp.com" To: CCL Subject: CCL: rmsd problem Message-Id: <-36869-080430091029-2339-bqt6tQbimxDN+2QR9EZrdg() server.ccl.net> X-Original-From: "Andrew Henry" Content-Language: en-gb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Apr 2008 13:40:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Andrew Henry" [ahenry-$-chemcomp.com] Dear Sobia, I think the problem is that the dock_rmsd.svl script was designed for comparing docked ligands with the known bound conformation of the same ligand from an X-ray structure. If you would like to measure a RMS deviation between ligands which share a common substructure, you could use fragment_rmsd.svl which uses a SMARTS query to identify pairs of atoms from the two ligands, and then calculates an RMS deviation for just those atoms. This script is available to download from http://svl.chemcomp.com/filedetails.php?lid=371&cid=54 I will send a copy of fragment_rmsd.svl to you in a separate email. Best wishes Andrew Henry Support Scientist Chemical Computing Group Cambridge, UK Tel: +44 1223 422321 Fax: +44 1223 422318 email: support^chemcomp.com -----Original Message----- > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] Sent: 30 April 2008 11:49 To: Altenhofen, Wolfram Subject: CCL: rmsd problem 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.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Apr 30 11:48:01 2008 From: "Kaci Tizi_Ouzou kaci.tiziouzou*_*gmail.com" To: CCL Subject: CCL: Vasp related tools Message-Id: <-36870-080430101504-17486-Nf7/pSDarmhUDSuEnDy/OQ!^!server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_13918_18296940.1209561541461" Date: Wed, 30 Apr 2008 07:18:59 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou]-[gmail.com] ------=_Part_13918_18296940.1209561541461 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi folks, I have started using Vasp to do a study in heterogenous catalysis. So far, I have figured how to model a crystal (surface). I am currently stuck since when I put a molecule on top of the surface, the software does not like it (complaining distances between atoms are small). (1) Question: Is there any tool I can use (before runing Vasp) to check whether my distances are all right? (2) If someone on this could share with me an input file (that works :-) that will be great. Thanks all Cheers Kaci ------=_Part_13918_18296940.1209561541461 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi folks,


I have started using Vasp to do a study in heterogenous catalysis. So far, I have figured how to model a crystal (surface).

I am currently stuck since when I put a molecule on top of the surface, the software does not like it (complaining distances between atoms are small).


(1) Question: Is there any tool I can use (before runing Vasp) to check whether my distances are all right?

(2) If someone on this could share with me an input file (that works :-)  that will be great.


Thanks all

Cheers


Kaci

------=_Part_13918_18296940.1209561541461-- From owner-chemistry@ccl.net Wed Apr 30 12:25:00 2008 From: "Attila Bende bende]-[itim-cj.ro" To: CCL Subject: CCL:G: ONIOM with Counterpoise correction? Message-Id: <-36871-080430102157-21098-554A4mNhGfU5d+v3ygu7tA(_)server.ccl.net> X-Original-From: "Attila Bende" Date: Wed, 30 Apr 2008 10:21:53 -0400 Sent to CCL by: "Attila Bende" [bende ~~ itim-cj.ro] Hi, Is it possible to perform Counterpoise correction calculation with ONIOM method using Gaussian03? If Yes, how it should be construct the input file? Many thanks Attila From owner-chemistry@ccl.net Wed Apr 30 12:58:01 2008 From: "Manish Sud msud|san.rr.com" To: CCL Subject: CCL: New release of MayaChemTools package Message-Id: <-36872-080430114159-15930-oL06UMTwNkbLmtknmmkdIA(_)server.ccl.net> X-Original-From: "Manish Sud" Date: Wed, 30 Apr 2008 11:41:54 -0400 Sent to CCL by: "Manish Sud" [msud+/-san.rr.com] A new release of MayaChemTools, a growing collection of Perl scripts and modules/classes to support day-to-day computational discovery needs, is available as free software; you can redistribute it and/or modify it under the terms of the GNU LGPL. The new scripts are: o PathLengthFingerprints.pl o CalculateSimilarityMatrixSDFiles.pl o CalculateSimilarityMatrixTextFiles.pl o InfoFingerprintsTextFiles.pl o InfoFingerprintsSDFiles.pl The new classes are: Atom.pm, Bond.pm, Molecule.pm, Graph.pm, CyclesDetection.pm, BitVector, Vector.pm, and so on. In addition, a variety of enhancements have been made to existing scripts. For further details and to download the package, please visit: www.MayaChemTools.org. The current focus of MayaChemTools research, development and implementation is similarity analysis. Stay tuned for similar similarity support scripts down the road. In the mean time, enjoy the current scripts. Your feedback is welcome. Manish Sud msud * san.rr.com From owner-chemistry@ccl.net Wed Apr 30 13:34:00 2008 From: "Andrew J Adamczyk a-adamczyk ~ northwestern.edu" To: CCL Subject: CCL:G: Cyclotrisilanylsilylene geometry optimization Message-Id: <-36873-080430114840-18997-TG2+hfTb0BVGEE5Z/JcNBA:_:server.ccl.net> X-Original-From: "Andrew J Adamczyk" Date: Wed, 30 Apr 2008 11:48:37 -0400 Sent to CCL by: "Andrew J Adamczyk" [a-adamczyk .. northwestern.edu] Hello, I am having difficulty isolating the minimum geometry of cyclotrisilanylsilylene on the B3LYP/6-31G* potential energy surface. My optimization shows a very strong driving force to form a four-member ring (Please see input and local minimum geometries using no symmetry and normal convergence criteria below) Starting geometry Si -1.544756000 4.612707000 -5.931502000 H -1.973140000 5.910459000 -5.940217000 Si -3.499370000 3.527761000 -5.645872000 H -3.938084000 1.954146000 -5.566826000 Si -4.119187000 5.530371000 -4.569900000 H -3.037664000 6.449871000 -4.123471000 H -5.307050000 5.603416000 -3.677955000 Si -4.366735000 5.332653000 -6.906301000 H -5.705811000 5.212335000 -7.541904000 H -3.423349000 6.114448000 -7.750889000 Final geometry B3LYP/6-31G* geometry from Gaussian 03 geometry optimization (no imaginary frequencies found) Si -1.756564000 4.078635000 -6.965815000 H -1.235307000 5.412168000 -6.428444000 Si -3.063223000 3.791924000 -5.070857000 H -4.077155000 2.693340000 -5.250129000 Si -4.435410000 5.557860000 -4.453891000 H -3.800659000 6.790560000 -3.923798000 H -5.763648000 5.291412000 -3.841928000 Si -4.068850000 5.305034000 -6.793432000 H -5.193892000 4.756925000 -7.587864000 H -3.520437000 6.570307000 -7.338679000 I have also tried applying Cs symmetry planes (with symm=loose) but I end up with a transition state which upon IRC calculations returns to the above local minimum. Your expertise would greatly be appreciated. Thank you very much, Andrew J. Adamczyk a-adamczyk^^^northwestern.edu Northwestern University, USA From owner-chemistry@ccl.net Wed Apr 30 14:10:01 2008 From: "Prashant Kumar prashantkbio .. gmail.com" To: CCL Subject: CCL: rmsd problem Message-Id: <-36874-080430112456-2252-thytXFEl2Yy3jjI1HZ1OzQ,,server.ccl.net> X-Original-From: "Prashant Kumar" Content-Type: multipart/alternative; boundary="----=_Part_1487_13977190.1209565261378" Date: Wed, 30 Apr 2008 19:51:01 +0530 MIME-Version: 1.0 Sent to CCL by: "Prashant Kumar" [prashantkbio^^gmail.com] ------=_Part_1487_13977190.1209565261378 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Sobia, Well I have faced the same problem so I suggest to use chimera its free (open source ) and can be downloaded from UCSF site , ther tou can choose some common subsets fragments and do the calculation. On Wed, Apr 30, 2008 at 6:52 PM, Dominic Ryan dominic.ryan^_^comcast.net < owner-chemistry!A!ccl.net> wrote: > > Sent to CCL by: Dominic Ryan [dominic.ryan%a%comcast.net] > Hello Sobia, > > Your problem is ill-defined. To calculate an rmsd you have to tell it > what atoms to use for the distance measurement. If you use two > conformations of the same molecule one can assume that all atoms are to be > used, mapping topologically identical atoms. If the molecules are different > you will have to decide which ones should be the basis for your comparison. > You could consider a scaffold core, or perhaps you have a key set of > functional groups that you view as critical, or perhaps you would be > interested in a center of mass for a coarser assessment. > Dominic Ryan > > sobia ahsan halim sobia_halim[a]yahoo.com wrote: > > > 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.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_1487_13977190.1209565261378 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Sobia,
                      Well I have faced the same problem so I suggest to use chimera its free (open source ) and can be downloaded from UCSF site , ther tou can choose some common subsets fragments and do the calculation.

On Wed, Apr 30, 2008 at 6:52 PM, Dominic Ryan dominic.ryan^_^comcast.net <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: Dominic Ryan [dominic.ryan%a%comcast.net]
Hello Sobia,

Your problem is ill-defined.  To calculate an rmsd you have to tell it what atoms to use for the distance measurement.  If you use two conformations of the same molecule one can assume that all atoms are to be used, mapping topologically identical atoms.  If the molecules are different you will have to decide which ones should be the basis for your comparison.
You could consider a scaffold core, or perhaps you have a key set of functional groups that you view as critical, or perhaps you would be interested in a center of mass for a coarser assessment.
Dominic Ryan

sobia ahsan halim sobia_halim[a]yahoo.com wrote:
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.>






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------=_Part_1487_13977190.1209565261378-- From owner-chemistry@ccl.net Wed Apr 30 16:58:00 2008 From: "Aron Walsh aronjwalsh++gmail.com" To: CCL Subject: CCL: Vasp related tools Message-Id: <-36875-080430132115-21436-NU+8q9o9whxB1fZ7Iley0g!=!server.ccl.net> X-Original-From: "Aron Walsh" Content-Type: multipart/alternative; boundary="----=_Part_2328_10974987.1209572710228" Date: Wed, 30 Apr 2008 10:25:10 -0600 MIME-Version: 1.0 Sent to CCL by: "Aron Walsh" [aronjwalsh _ gmail.com] ------=_Part_2328_10974987.1209572710228 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Kaci, It sounds like you may have mixed up the coordinate system in your structure file. When you added the molecule check whether the coordinates are cartesian or fractional. By default VASP outputs fractional in CONTCAR, even when your initial structure (POSCAR) was in cartesian. VESTA is a very useful (and free) tool for visualizing structures from VASP and other periodic codes: http://www.geocities.jp/kmo_mma/crystal/en/vesta.html Good luck! Aron On Wed, Apr 30, 2008 at 7:18 AM, Kaci Tizi_Ouzou kaci.tiziouzou*_*gmail.com< owner-chemistry!=!ccl.net> wrote: > Hi folks, > > > I have started using Vasp to do a study in heterogenous catalysis. So far, > I have figured how to model a crystal (surface). > > I am currently stuck since when I put a molecule on top of the surface, > the software does not like it (complaining distances between atoms are > small). > > > (1) Question: Is there any tool I can use (before runing Vasp) to check > whether my distances are all right? > > (2) If someone on this could share with me an input file (that works :-) > that will be great. > > > Thanks all > > Cheers > > > Kaci > > ------=_Part_2328_10974987.1209572710228 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Kaci,

It sounds like you may have mixed up the coordinate system in your structure file. When you added the molecule check whether the coordinates are cartesian or fractional. By default VASP outputs fractional in CONTCAR, even when your initial structure (POSCAR) was in cartesian.

VESTA is a very useful (and free) tool for visualizing structures from VASP and other periodic codes: http://www.geocities.jp/kmo_mma/crystal/en/vesta.html

Good luck!

Aron


On Wed, Apr 30, 2008 at 7:18 AM, Kaci Tizi_Ouzou kaci.tiziouzou*_*gmail.com <owner-chemistry!=!ccl.net> wrote:
Hi folks,


I have started using Vasp to do a study in heterogenous catalysis. So far, I have figured how to model a crystal (surface).

I am currently stuck since when I put a molecule on top of the surface, the software does not like it (complaining distances between atoms are small).


(1) Question: Is there any tool I can use (before runing Vasp) to check whether my distances are all right?

(2) If someone on this could share with me an input file (that works :-)  that will be great.


Thanks all

Cheers


Kaci


------=_Part_2328_10974987.1209572710228--