From chemistry-request@server.ccl.net Wed Nov 13 03:14:24 2002 Received: from oulu.fi ([130.231.240.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAD8EOD28367 for ; Wed, 13 Nov 2002 03:14:24 -0500 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id KAA13409 for ; Wed, 13 Nov 2002 10:14:23 +0200 (EET) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id KAA28300 for ; Wed, 13 Nov 2002 10:05:09 +0200 (EET) Date: Wed, 13 Nov 2002 10:05:09 +0200 (EET) From: =?ISO-8859-1?Q?Atte_Sillanp=E4=E4?= X-X-Sender: asillanp@paju.oulu.fi Reply-To: atte.sillanpaa@oulu.fi To: chemistry@ccl.net Subject: Re: CCL:change the PCM atom radii in Gaussian98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 12 Nov 2002, Cust. Service Doug wrote: > > Atte, > > the manual is incorrect that more than two lines can be supplied > for SCRF=(CPCM,Read) but you can specify multiple options per line > so just combine your options onto two lines and they will all be > read. The best way to modify individual radii is with the NSFE=n > option which reads in a list of radii for each of the atoms, or > each sphere if you have combined multiple atoms in a sphere. Here > is an example, > > #P SCRF=(PCM,Read,Dielectric=15.0) HF/3-21G Test > > NH3 > > 0 1 > N > X 1 1.0 > H 1 rNH 2 A > H 1 rNH 2 A 3 120.0 > H 1 rNH 2 A 3 -120.0 > > rNH 1.0 > A 109.0 > > TSAre=0.4 NSFE=1 > dump > > 1 1.770 1.3 > > I have used a single sphere, the same as the UAHF model, but scaled at 1.3. Thank you for the prompt answer. The maximum of two lines for the additional keywords solves the problem. However, I'd like to point out the reason for the other difficulties I've had thus far. The use of NFSE keyword does not work (G98 ignores it) if you specify the solvent in the route section using (solvent=water). NFSE is read and used if the solvent is specified using (dielectric=78.39) in the route section. According to the manual, this keyword is for the dipole model. I guess (correct me if I'm wrong) that water can be specified for the PCM-model also by adding the following keywords in the additional input section: eps=78.39 rsolv=1.385. (As these are the default values, they can be omitted.) Eps=78.39 only in the additional input is not enough, because if (Dielectric=xxx) is omitted from the route section, the NFSE input is ignored, too. So, in summary, if you want to use your own radii, you can do this by using the scrf(Dielectric=xx,Read) in the route section, and then by specifying the radii at atomic centers as Doug suggested in his email. Adding dump is also good to check in a bit more detail what values are actually used. Thanks for all answers! Cheers, atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Wed Nov 13 03:52:22 2002 Received: from hamlin.cc.boun.edu.tr ([193.140.192.230]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAD8qID29364 for ; Wed, 13 Nov 2002 03:52:22 -0500 Received: by hamlin.cc.boun.edu.tr (Postfix, from userid 757) id 26CAB1FDB; Wed, 13 Nov 2002 10:49:49 +0200 (EET) Received: from localhost (localhost [127.0.0.1]) by hamlin.cc.boun.edu.tr (Postfix) with ESMTP id EF2851C0B for ; Wed, 13 Nov 2002 10:49:48 +0200 (EET) Date: Wed, 13 Nov 2002 10:49:48 +0200 (EET) From: Nurcan Senyurt X-Sender: senyurtn@hamlin.cc.boun.edu.tr To: chemistry@ccl.net Subject: Script for calculating Eckart Potential Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I want to calculate the tunneling correction by the Eckart potential. I tried to write a script, but unfortunately I could not implement some integrals in the programme. I will appreciate if you have any script to calculate tuneneling correction by the Eckart potential. Thank you in advance. Nurcan Senyurt Tuzun From chemistry-request@server.ccl.net Wed Nov 13 07:21:43 2002 Received: from mail.mersin.edu.tr ([193.255.128.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADCLdD01540 for ; Wed, 13 Nov 2002 07:21:41 -0500 Received: from localhost (localhost.mersin.edu.tr [127.0.0.1]) by mail.mersin.edu.tr (Postfix) with ESMTP id EA7074C6 for ; Wed, 13 Nov 2002 14:30:08 +0200 (EET) Received: from 10.0.6.34 (localhost.mersin.edu.tr [127.0.0.1]) by mail.mersin.edu.tr (Postfix) with SMTP id 3AF554BB for ; Wed, 13 Nov 2002 14:30:08 +0200 (EET) Message-ID: X-Mailer: BasiliX 1.1.0 -- http://basilix.org X-SenderIP: 10.0.6.34 Date: Wed, 13 Nov 2002 14:30:08 EET From: Hatice Can Reply-To: haticecan@mersin.edu.tr Subject: SCF=Restart problem To: chemistry@ccl.net X-Virus-Scanned: by AMaViS perl-11 Dear CCL Memebers, I have tried to use SCF=Restart option, when I have performed CASSCF calculations. But, I noticed that it can not restart. My route line is as below. All the suggestions will be appricated. Many thanks in advance and kind regards. Hatice The route line: -#- MaxDisk=480MW %NoSave %Chk=zeorb.chk #T CAS(16,12,NRoot=2)/3-21G* Gues=Read Test MP2=Full SCF=Restart # Geom=Check Charge From chemistry-request@server.ccl.net Wed Nov 13 01:08:34 2002 Received: from atcmail.atc.tcs.co.in ([203.199.176.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAD68CQ26626 for ; Wed, 13 Nov 2002 01:08:18 -0500 Received: from ATCSWETANIGAM (sweta_t.atc.tcs.co.in [172.19.40.166]) by atcmail.atc.tcs.co.in (8.11.0/8.11.0) with SMTP id gAD6A5V11504; Wed, 13 Nov 2002 11:40:05 +0530 Message-ID: <009d01c28adb$380f8f90$a62813ac@hydbad.tcs.co.in> From: "sweta nigam" To: Cc: "priya" Subject: COMFA...could you help? Date: Wed, 13 Nov 2002 11:39:26 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_009A_01C28B09.51B247C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_009A_01C28B09.51B247C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi All I am working on COMFA & need some guideline regarding this " what is the type/ form of gaussian function (s) used for estimating = the Field based Shape similarity " for allignment in COMFA Thanks n Regards Sweta=20 TCS ------=_NextPart_000_009A_01C28B09.51B247C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi All
   I am working on COMFA = & need some=20 guideline regarding this
" what is the type/ form of gaussian = function (s)=20 used for estimating the
Field based Shape similarity " for allignment = in=20 COMFA

Thanks n Regards
Sweta
TCS
------=_NextPart_000_009A_01C28B09.51B247C0-- From chemistry-request@server.ccl.net Wed Nov 13 03:41:43 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAD8fgD28955 for ; Wed, 13 Nov 2002 03:41:43 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H5I002FIAF6T8@mailstudenti.unimi.it> for chemistry@ccl.net; Wed, 13 Nov 2002 09:33:06 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H5I00EQ2AF6KF@smtp.unimi.it> for chemistry@ccl.net; Wed, 13 Nov 2002 09:33:07 +0100 (MET) Date: Wed, 13 Nov 2002 09:35:08 +0100 From: Giulio Vistoli Subject: Re: CCL:software for ligand-receptor interaction energy evaluation ? To: Nikolaus Stiefl , chemistry@ccl.net Message-id: <003901c28aef$92a63c60$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <1037121298.3dd13712472b1@webmail.uni-wuerzburg.de> Dear Nikolaus Your collegue can try VEGA (free downloadable at http://www.ddl.unimi.it). This program is able to calculate the interaction energy between ligand and receptor using CVFF forcefield. Moreover it splits this value in its components (electrostatic, Lennard-Jones) and calculate the interaction energy per residue. Finally in Win32 version it shows the residues that have an energy greater than a user defined cutoff in order to aid the complex analysis. Best regards Giulio Vistoli --------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it ----- Original Message ----- From: "Nikolaus Stiefl" To: Sent: Tuesday, November 12, 2002 6:14 PM Subject: CCL:software for ligand-receptor interaction energy evaluation ? > Hi, > > a colleague of mine asked me if I could calculate interaction energies between > a ligand and a receptor into which he docked some compounds. > > I had a look at some of the complexes and it seems like he wants to use this > for a reevaluation of the activity of his docked structures. > > Unfortunately I am not too much into this sort of energy calculations and now I > am looking for a freeware program that is able to do that with not too much > effort. > > I would be very grateful if anybody could point me into a direction. > > Cheers > Nik > -- > Nikolaus Stiefl > Chemometriks and Drug Design > University Wuerzburg > Dept. of Pharmacy > Am Hubland > D-97074 Wuerzburg > Germany > Phone: +49 - 931 8885473 > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Nov 13 08:22:05 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADDM5D02326 for ; Wed, 13 Nov 2002 08:22:05 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id gADDM5b29324; Wed, 13 Nov 2002 08:22:05 -0500 (EST) Date: Wed, 13 Nov 2002 08:22:05 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: NMR-based Metabonomics with Multivariate Data Analysis (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT Date: Wed, 13 Nov 2002 13:42:47 +0100 From: Gun Johansson To: "'jkl@ccl.net'" Subject: NMR-based Metabonomics with Multivariate Data Analysis Time for a Umetrics & Metabometrix course with a special profile: Welcome to the course "NMR-based Metabonomics with Multivariate Data Analysis" in USA, Parsippany NJ. The course is designed to provide a theoretical background in NMR-based Metabonomics and covers recent applications of this technique in the fields of toxicology, drug metabolism and food science. The course is three days, 14-16 January 2003. For more information, please review your invitation at Umetrics website: http://www.umetrics.com/pdfs/courses/NMR_Metabonom_030114-16.pdf We look forward to your application. Best regards, Umetrics AB Gun Johansson ______________________________________ Gun Johansson Course Administrator Umetrics AB, Box 7960, SE-90719 Umeå, Sweden Tel: +46(0)90 184854 Fax: +46(0)90 184899 Mailto:gun.johansson@umetrics.com Visit http://www.umetrics.com From chemistry-request@server.ccl.net Wed Nov 13 04:32:32 2002 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAD9WVD30618 for ; Wed, 13 Nov 2002 04:32:32 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id KAA14381 for ; Wed, 13 Nov 2002 10:32:30 +0100 Received: (qmail 7858 invoked by uid 525); 13 Nov 2002 09:32:31 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 13 Nov 2002 09:32:31 -0000 Date: Wed, 13 Nov 2002 10:32:31 +0100 (CET) From: To: Nikolaus Stiefl cc: chemistry@ccl.net Subject: Re: CCL:software for ligand-receptor interaction energy evaluation ? In-Reply-To: <1037121298.3dd13712472b1@webmail.uni-wuerzburg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, > a colleague of mine asked me if I could calculate interaction energies between > a ligand and a receptor into which he docked some compounds. There are many options: 1) AutoDock can calculate the energy of a complex using the command mode. http://www.scripps.edu/pub/olson-web/doc/autodock/ 2) There is a new program: X-cscore (Wang et al, 2002) 3) Vega http://users.unimi.it/ddl/vega/manual/index.htm etc. I have tried 1) and 2), both of them are easy-to-use. These methods can be used for rapid estimations of binding energy. There are also other techniques, based on MD, etc., which requires more time. Best wishes, Csaba From chemistry-request@server.ccl.net Wed Nov 13 05:36:54 2002 Received: from antivirus.unimo.it ([155.185.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADAarD31853 for ; Wed, 13 Nov 2002 05:36:53 -0500 Received: from mail.unimo.it (mail.unimo.it [155.185.1.1]) by antivirus.unimo.it (8.12.5/8.12.5) with ESMTP id gADAarR4027372 for ; Wed, 13 Nov 2002 11:36:53 +0100 Received: from unimo.it (cleopatra.unimo.it [155.185.29.69]) by mail.unimo.it (2.1.2/8.9.1/Execmail 2.1) with ESMTP id LAA1623531 for ; Wed, 13 Nov 2002 11:36:52 +0100 (CET) Message-ID: <3DD22AEA.2020506@unimo.it> Date: Wed, 13 Nov 2002 11:35:22 +0100 From: anna ferrari User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.0.0) Gecko/20020606 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: MPI dock5.1 Content-Type: multipart/alternative; boundary="------------080709000205060909010403" X-Virus-Scanned: by amavisd-milter (http://amavis.org/) --------------080709000205060909010403 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi I'm running an MPI dock 5.1.0 on a linux machine but I have some problems. If I run the job on a _single processor_ with the following _input file_ --------------------------------------- ligand_atom_file xtal-lig.mol2 ligand_outfile_prefix xtal-lig-3n write_orientations yes write_conformations yes calculate_rmsd yes rank_ligands no max_send_queue_size 10 max_recv_queue_size 10000 orient_ligand yes automated_matching yes receptor_site_file spheres_use max_orientations 1000 flexible_ligand no bump_filter yes bump_grid_prefix ../rec_linux max_bumps 3 score_molecules yes contact_score_primary no contact_score_secondary no energy_score_primary yes energy_score_secondary yes vdw_scale 1 es_scale 1 nrg_grid_prefix ../rec_linux minimize_ligand yes minimze_rigid_anchor yes minimze_layer_growth yes minimze_final_pose yes minimze_final_pose_rigid no minimze_final_pose_torsions no minimize_final_pose_complete yes minimizer_choice 0 initial_translation 1.0 initial_rotation 1.0 initial_torsion 10.0 maximum_iterations 100 maximum_function_calls 100000 window_based_termination no scaled_range_termination no multiple_simplex_cycles no random_number_generator 0 random_number_seed 2002 atom_model all vdw_defn_file vdw.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl calc_internal_energy no max_ranked_ligands 100 scored_mol_output_override yes gbsa_score_secondary no --------------------------------------- * dock doesn't process any molecule writing this _output file_* --------------------------------------- DOCK v5.1.0 Released 10-15-2002 Copyright UCSF Authored by: Tack Kuntz Demetri Moustakas Scott Pegg Fernando Martin -------------------------------------- Molecule Library Parameters ------------------------------------------------------------------------------------------ ligand_atom_file pm_prova.mol2 ligand_outfile_prefix pm_prova write_orientations no write_conformations no calculate_rmsd no rank_ligands yes max_ranked_ligands 100 scored_mol_output_override yes max_send_queue_size 20 max_recv_queue_size 1000 Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand yes automated_matching no distance_tolerence 0.3 distance_minimum 0.5 nodes_minimum 3 nodes_maximum 4 receptor_site_file spheres_use max_orientations 1000 Anchor & Grow Parameters ------------------------------------------------------------------------------------------ flexible_ligand no Bump Filter Parameters ------------------------------------------------------------------------------------------ bump_filter yes bump_grid_prefix ../rec_linux Master Score Parameters ------------------------------------------------------------------------------------------ score_molecules yes Contact Score Paramters ------------------------------------------------------------------------------------------ contact_score_primary no contact_score_secondary no Energy Score Parameters ------------------------------------------------------------------------------------------ energy_score_primary yes energy_score_secondary no vdw_scale 1 es_scale 1 nrg_grid_prefix ../rec_linux GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_score_secondary no Warning: No secondary scoring function selected. Primary scoring function will be used as secondary. General Optimization Parameters -------------------------------------------------------------------------------- minimize_ligand yes minimze_rigid_anchor no minimze_layer_growth no minimze_final_pose yes minimze_final_pose_rigid no minimze_final_pose_torsions no minimize_final_pose_complete yes minimizer_choice 0 Simplex Optimization Parameters ------------------------------------------------------------------------------- initial_translation 1.0 initial_rotation 1.0 initial_torsion 10.0 maximum_iterations 100 maximum_function_calls 500 window_based_termination no scaled_range_termination no multiple_simplex_cycles no Random Number Generation Parameters ------------------------------------------------------------------------------- random_number_generator 0 random_number_seed 2002 Molecule Parameters ------------------------------------------------------------------------------------------ atom_model all vdw_defn_file vdw.defn.old flex_defn_file flex.defn flex_drive_file flex_drive.tbl calc_internal_energy no ------------------------------------------------------------------------------------------ Initializing Library File Routines... Initializing Orienting Routines... Initializing Bump Filter Routines... Reading the bump grid from ../rec_linux.bmp Initializing Energy Score Routines... Reading the energy grid from ../rec_linux.nrg *0 Molecules Processed* -Running an MPI job using _four processors_ and the same input file, this is the final message: *0 Molecules Processed WARNING assign_vdw_labels: No vdw parameters for 1 C3 p3_11707: p4_error: interrupt SIGSEGV: 11 * after writing four times the input parameters. My command line is a dock.com file --------------------------------- #!/bin/tcsh #PBS -l nodes=1:ppn=1,walltime=48:00:00 cd /home/giulio/anna/search mpirun -np 1 -machinefile $PBS_NODEFILE /home/giulio/dock5/dock_5.1.0/bin/dock5.linux -i dock.in > dock.out --------------------------------------------------------------------------------------- Any suggestion? Thank you in advance Anna --------------080709000205060909010403 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi
I'm running an MPI dock 5.1.0 on a linux machine but I have some problems.

If I run the job on a single processor with the following input file

---------------------------------------
ligand_atom_file                 xtal-lig.mol2
ligand_outfile_prefix          xtal-lig-3n
write_orientations                 yes
write_conformations            yes
calculate_rmsd                      yes
rank_ligands                           no
max_send_queue_size            10
max_recv_queue_size            10000
orient_ligand                         yes
automated_matching             yes
receptor_site_file                 spheres_use
max_orientations                 1000
flexible_ligand                     no
bump_filter                         yes
bump_grid_prefix               ../rec_linux
max_bumps                         3
score_molecules                  yes
contact_score_primary          no
contact_score_secondary        no
energy_score_primary           yes
energy_score_secondary         yes
vdw_scale                             1
es_scale                                 1
nrg_grid_prefix                ../rec_linux
minimize_ligand                yes
minimze_rigid_anchor           yes
minimze_layer_growth           yes
minimze_final_pose                 yes
minimze_final_pose_rigid         no
minimze_final_pose_torsions    no
minimize_final_pose_complete   yes
minimizer_choice                        0
initial_translation                     1.0
initial_rotation                          1.0
initial_torsion                          10.0
maximum_iterations                100
maximum_function_calls         100000
window_based_termination       no
scaled_range_termination          no
multiple_simplex_cycles           no
random_number_generator        0
random_number_seed             2002
atom_model                     all
vdw_defn_file                  vdw.defn
flex_defn_file                 flex.defn
flex_drive_file                flex_drive.tbl
calc_internal_energy           no
max_ranked_ligands             100
scored_mol_output_override     yes
gbsa_score_secondary           no
---------------------------------------

dock doesn't process any molecule writing this output file

---------------------------------------
DOCK v5.1.0

Released 10-15-2002
Copyright UCSF
Authored by:
        Tack Kuntz
        Demetri Moustakas
        Scott Pegg
        Fernando Martin
--------------------------------------


Molecule Library Parameters
------------------------------------------------------------------------------------------
ligand_atom_file               pm_prova.mol2
ligand_outfile_prefix          pm_prova
write_orientations             no
write_conformations            no
calculate_rmsd                 no
rank_ligands                   yes
max_ranked_ligands             100
scored_mol_output_override     yes
max_send_queue_size            20
max_recv_queue_size            1000

Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                  yes
automated_matching             no
distance_tolerence             0.3
distance_minimum               0.5
nodes_minimum                  3
nodes_maximum                  4
receptor_site_file             spheres_use
max_orientations               1000

Anchor & Grow Parameters
------------------------------------------------------------------------------------------
flexible_ligand                no

Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                    yes
bump_grid_prefix               ../rec_linux

Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                yes

Contact Score Paramters
------------------------------------------------------------------------------------------
contact_score_primary          no
contact_score_secondary        no

Energy Score Parameters
------------------------------------------------------------------------------------------
energy_score_primary           yes
energy_score_secondary         no
vdw_scale                      1
es_scale                       1
nrg_grid_prefix                ../rec_linux

GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_score_secondary           no

Warning:  No secondary scoring function selected.  Primary scoring function will be used as secondary.


General Optimization Parameters
--------------------------------------------------------------------------------
minimize_ligand                yes
minimze_rigid_anchor           no
minimze_layer_growth           no
minimze_final_pose             yes
minimze_final_pose_rigid       no
minimze_final_pose_torsions    no
minimize_final_pose_complete   yes
minimizer_choice               0

Simplex Optimization Parameters
-------------------------------------------------------------------------------
initial_translation            1.0
initial_rotation               1.0
initial_torsion                10.0
maximum_iterations             100
maximum_function_calls         500
window_based_termination       no
scaled_range_termination       no
multiple_simplex_cycles        no

Random Number Generation Parameters
-------------------------------------------------------------------------------
random_number_generator        0
random_number_seed             2002

Molecule Parameters
------------------------------------------------------------------------------------------
atom_model                     all
vdw_defn_file                  vdw.defn.old
flex_defn_file                 flex.defn
flex_drive_file                flex_drive.tbl
calc_internal_energy           no
------------------------------------------------------------------------------------------

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Bump Filter Routines...
 Reading the bump grid from ../rec_linux.bmp
Initializing Energy Score Routines...
 Reading the energy grid from ../rec_linux.nrg


0 Molecules Processed



-Running an MPI job using four processors and the same input file, this is the final message:

0 Molecules Processed
WARNING assign_vdw_labels: No vdw parameters for 1  C3
p3_11707:  p4_error: interrupt SIGSEGV: 11

after writing four times the input parameters.

My command line is a dock.com file
---------------------------------
#!/bin/tcsh
#PBS -l nodes=1:ppn=1,walltime=48:00:00


cd /home/giulio/anna/search
mpirun -np 1 -machinefile $PBS_NODEFILE /home/giulio/dock5/dock_5.1.0/bin/dock5.linux -i dock.in > dock.out
---------------------------------------------------------------------------------------

Any suggestion?

Thank you in advance
Anna



--------------080709000205060909010403-- From chemistry-request@server.ccl.net Wed Nov 13 14:27:22 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADJRMD10061 for ; Wed, 13 Nov 2002 14:27:22 -0500 Received: from chem.iupui.edu ([134.68.137.128]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id OAA3294475; Wed, 13 Nov 2002 14:26:49 -0500 (EST) Message-ID: <3DD2B582.BA95AC7C@chem.iupui.edu> Date: Wed, 13 Nov 2002 14:31:19 -0600 From: "Boyd, D." X-Mailer: Mozilla 4.79C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: "Glossman-Mitnik, Daniel (Mex.)" CC: OSC CCL Subject: re: molecular computational chemistry Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Dr. Glossman-Mitnik, There are been a number of essays on the emergence of the field of computational chemistry. The references below are relevant. K. B. Lipkowitz and D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. vii- xii. Preface (on the Meaning and Scope of Computational Chemistry). D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 461-479. The Computational Chemistry Literature. J. D. Bolcer and R. B. Hermann, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1994, Vol. 5, pp. 1- 63. The Development of Computational Chemistry in the United States. D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1995, Vol. 6, pp. 317-354. Molecular Modeling Software in Use: Publication Trends. D. B. Boyd and K. B. Lipkowitz, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 14, pp. 399- 439. History of the Gordon Research Conferences on Computational Chemistry. D. B. Boyd and K. B. Lipkowitz, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, Hoboken, NJ, 2002, Vol. 18, pp. 293- 319. Appendix: Examination of the Employment Environment for Computational Chemistry. I hope these references are helpful. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Research Professor of Chemistry Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Nov 13 08:49:24 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADDnOD03320 for ; Wed, 13 Nov 2002 08:49:24 -0500 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id IAA04682; Wed, 13 Nov 2002 08:49:17 -0500 (EST) Message-ID: <3DD25849.8D6A9A9B@cornell.edu> Date: Wed, 13 Nov 2002 07:48:57 -0600 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Whom to teach what continued... young pretenders or experienced hands.. References: Content-Type: multipart/alternative; boundary="------------9AD5AB4CDEF08E2041410A9C" --------------9AD5AB4CDEF08E2041410A9C Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I still say that computational chemistry/molecular modelling is a sub-branch of physical chemistry, just as alkene synthesis is a sub-branch of organic synthesis. Richard James Robinson wrote: > So the debate continues. Most people seem to agree with the general > principle that Computational chemistry/Molecular modelling (change > description to suit personal taste) is a science in its own right. The > scientists doing the computational work need to communicate > effectively and understand exactly what is required (yes, no, 18 digit > numbers, pretty pictures…) > > So if starting from scratch, say you grabbed some unsuspecting student > and tried to teach them… where would you start? Is there a general > foundation to it all? (If only Charles Babbage and Erwin Schrodinger > had email addresses..) The people I have met tended to do first > degrees in science, computer sciences or maths and then moved into > computational chemistry through jobs in industry/academia and > postgraduate study. So there is an added advantage. They have > experience of real science before attempting the computation. > > Is the best way, through experience and evolution or would it actually > be okay to do it from scratch at the age of 18 or so… > > With higher education becoming more expensive, I am sure the delight > of market forces will influence trends, .. science graduates will > become rarer.. unless salaries increase.. new modellers will have to > come from somewhere… > > That’s my 2 pence concluded. j > -- Richard L. Wood, Ph. D. Physical/Computational Chemist --------------9AD5AB4CDEF08E2041410A9C Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit  
I still say that computational chemistry/molecular modelling is a sub-branch of physical chemistry, just as alkene synthesis is a sub-branch of organic synthesis.

Richard

James Robinson wrote:

So the debate continues. Most people seem to agree with the general principle that Computational chemistry/Molecular modelling (change description to suit personal taste) is a science in its own right. The scientists doing the computational work need to communicate effectively and understand exactly what is required (yes, no, 18 digit numbers, pretty pictures…) 

So if starting from scratch, say you grabbed some unsuspecting student and tried to teach them… where would you start? Is there a general foundation to it all? (If only Charles Babbage and Erwin Schrodinger had email addresses..) The people I have met tended to do first degrees in science, computer sciences or maths and then moved into computational chemistry through jobs in industry/academia and postgraduate study. So there is an added advantage. They have experience of real science before attempting the computation. 

Is the best way, through experience and evolution or would it actually be okay to do it from scratch at the age of 18 or so… 

With higher education becoming more expensive, I am sure the delight of market forces will influence trends, .. science graduates will become rarer.. unless salaries increase.. new modellers will have to come from somewhere…

That’s my 2 pence concluded. j 

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
  --------------9AD5AB4CDEF08E2041410A9C-- From chemistry-request@server.ccl.net Wed Nov 13 08:40:50 2002 Received: from bfp.cc.purdue.edu ([128.210.189.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADDeoD03100 for ; Wed, 13 Nov 2002 08:40:50 -0500 Received: from bfp.cc.purdue.edu (localhost [127.0.0.1]) by bfp.cc.purdue.edu (8.12.5/8.12.5) with ESMTP id gADDeof0000453 for ; Wed, 13 Nov 2002 08:40:50 -0500 (EST) Received: from localhost (bfp@localhost) by bfp.cc.purdue.edu (8.12.5/8.12.5/Submit) with ESMTP id gADDeoFk000450 for ; Wed, 13 Nov 2002 08:40:50 -0500 (EST) X-Authentication-Warning: bfp.cc.purdue.edu: bfp owned process doing -bs Date: Wed, 13 Nov 2002 08:40:50 -0500 (EST) From: Bryan Putnam X-X-Sender: bfp@bfp.cc.purdue.edu To: CCL Subject: Benchmarks that correlate with Gaussian performance Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, Is anyone aware of any benchmark utilities (such as LINPACK, Whetstone, etc.) that would give a fairly good indication to a hardware vendor whether or not Gaussian performs well on their hardware, without the vendor actually having to have access to a copy of Gaussian? Thanks, Bryan -- Bryan Putnam, IT Research Computing Services Mathematical Sciences Building Email: bfp@purdue.edu 150 North University Street Phone: 765.496.8225 West Lafayette, IN 47907-2068 Fax: 765.494.0566 http://www.purdue.edu/ITaP http://www-rcd.cc.purdue.edu/~bfp/ From chemistry-request@server.ccl.net Wed Nov 13 12:03:09 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADH39D07253 for ; Wed, 13 Nov 2002 12:03:09 -0500 Received: from LAQUICOM02 (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id gADHsUi11102 for ; Wed, 13 Nov 2002 10:54:30 -0700 Message-ID: <00e801c28b2e$83c0c3c0$be00000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: Is Computational Chemistry a real science ? Date: Wed, 13 Nov 2002 10:05:40 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00E5_01C28AFC.388DBD40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00E5_01C28AFC.388DBD40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 On Tuesday, November 12, 2002, James Robinson wrote: ... So there is an added advantage. They have experience of real = science = before attempting the computation =20 Thus, Computational Chemistry is not a real science? Everyone in this list agrees with this assert ? Best regards Dr. Daniel Glossman-Mitnik *************************************************************************= *** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com *************************************************************************= *** ------=_NextPart_000_00E5_01C28AFC.388DBD40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

 
On Tuesday, November 12, 2002, James Robinson=20 wrote:

... So = there is an=20 added advantage. They have experience of real=20 = science           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;       =20 before=20 attempting the=20 computation

  
 
Thus,  Computational Chemistry is = not a real=20 science?
   Everyone in this list = agrees with this=20 assert ?
 
Best regards
 
          &nbs= p;            = ;        =20 Dr. Daniel Glossman-Mitnik
 
 
****************************************************************= ************
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigacion en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109 = -=20 Mexico
Phone: (52) 614 4391151      FAX: = (52) 614=20 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ******************************************************************=
------=_NextPart_000_00E5_01C28AFC.388DBD40-- From chemistry-request@server.ccl.net Wed Nov 13 15:19:07 2002 Received: from HUBBLE.PLEXXIKON.COM ([66.123.16.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gADKJ6D10657 for ; Wed, 13 Nov 2002 15:19:06 -0500 Received: by HUBBLE.PLEXXIKON.COM with Internet Mail Service (5.5.2653.19) id ; Wed, 13 Nov 2002 12:19:30 -0800 Message-ID: <17F87CDE995E3541BE60551DAB1B676246D175@HUBBLE.PLEXXIKON.COM> From: Fernando Martin To: "'chemistry@ccl.net'" Subject: Linking consecutive jobs in GAMESS Date: Wed, 13 Nov 2002 12:19:30 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, I am a newbie to GAMESS and currently coming to terms with this programs' features. I was wondering if anyone knew whether there is an analog to the GAUSSIAN "--link--" command which would permit that one submits consecutive jobs. Also I was wondering if anyone knew what the 'x' in the IFREEZ(x) command stands for. Thanks in advance, and I look forward to hearing your replies, Best regards, Fernando