Friends, I want to do docking of a drug molecule to a prot= ein in=C2=A0Autodock. I a want to convert the Gaussian 09w file to Auutodoc= k. But failed. I have the cartesian coordinate data, is it possible to conv= ert the cartesian data to Autodock/

partha

D= r. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyal= aya, Burdwan

--f403045c2454db5f28054f77b131-- From owner-chemistry@ccl.net Sun May 14 12:36:01 2017 From: "Igors Mihailovs igorsm[-]cfi.lu.lv" To: CCL Subject: CCL:G: Gaussian error Message-Id: <-52801-170513120117-27692-u1JLd+H3QOyfWbotyeBbDw__server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary="------------EC52B6CB3AC8C3CB4EC68999" Date: Sat, 13 May 2017 19:02:41 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm]![cfi.lu.lv] This is a multi-part message in MIME format. --------------EC52B6CB3AC8C3CB4EC68999 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Dear Amritpal, It would be highly beneficial if You share at least Your output file. Sincerely, Igors Mihailovs ISSP UL On 13/05/17 12:14, Amritpal ghumman amritpalghumman###gmail.com wrote: > I am getting this error in frequency calculations. Can you suggest me > some solution > > > Gaussian terminated with a non-zero exit status: 1 > ===POST-JOB OUTPUT FROM THE NSC g09 WRAPPER=== > Gaussian terminated with a non-zero exit status: 1 > Checking whether the scratch directory ran full: > Filesystem Size Used Avail Use% Mounted on > /dev/mapper/vg_scratch-lv_scratch > 442G 16G 404G 4% /scratch/local > > With best regards > Amritpal singh --------------EC52B6CB3AC8C3CB4EC68999 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Amritpal,

It would be highly beneficial if You share at least Your output file.

Sincerely,
Igors Mihailovs
ISSP UL

On 13/05/17 12:14, Amritpal ghumman amritpalghumman###gmail.com wrote:

I am getting this error in frequency calculations. Can you suggest me some solution

Gaussian terminated with a non-zero exit status: 1
===POST-JOB OUTPUT FROM THE NSC g09 WRAPPER===
Gaussian terminated with a non-zero exit status: 1
Checking whether the scratch directory ran full:
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg_scratch-lv_scratch
442G 16G 404G 4% /scratch/local

With best regards

Amritpal singh

--------------EC52B6CB3AC8C3CB4EC68999-- From owner-chemistry@ccl.net Sun May 14 13:11:01 2017 From: "Luca Frediani luca.frediani.:.uit.no" To: CCL Subject: CCL:G: Coding solvation workshop: extended deadline and IJQC special issue Message-Id: <-52802-170514040344-31759-rTq84aGTmQ2Gma2IlmX1qw,server.ccl.net> X-Original-From: Luca Frediani Content-Type: multipart/alternative; boundary="------------74E3837106F55DDA2B4949B5" Date: Sun, 14 May 2017 10:03:34 +0200 MIME-Version: 1.0 Sent to CCL by: Luca Frediani [luca.frediani[]uit.no] This is a multi-part message in MIME format. --------------74E3837106F55DDA2B4949B5 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Dear Andreas, it is indeed true the workshop does not feature anybody from the COSMO-RS community among the keynote speakers, and I am sorry you feel that COSMO has been left aside. I am however surprised by your post: six months ago, when I had the idea to organize the workshop, I sent you and many of our colleagues an email asking if you were interested in either organizing or participating. You clearly answered that you did not see how such a workshop "shall be helpful to anybody". I am glad to see that you changed your mind regarding the usefulness of our workshop, and I can assure you that if you or anybody else from the COSMO-RS community will subscribe and submit a relevant abstract, it will be included in the program. As stated in my original post, there are still spots available! Best regards, Luca Frediani >> Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de] >> What is a workshop on coding solvation worth, if it completely ignores >> the currently most accurate solvation model, i.e. COSMO-RS. >> >> Have fun with your workshop >> >> Andreas >> >> >> Am 12.05.2017 um 14:17 schrieb Luca Frediani luca.frediani()uit.no: >>> Sent to CCL by: "Luca Frediani" [luca.frediani%a%uit.no] >>> Dear Colleague, >>> >>> the registration for the "Coding solvation" workshop is still open, but >>> only a few spots are >>> still available at the venue hotel. Therefore, we strongly encourage >>> you to register soon. >>> >>> CONTRIBUTED PRESENTATIONS: The deadline to submit an abstract for a >>> contributed >>> presentation has now been extended to the 15th of June. >>> >>> IJQC SPECIAL ISSUE: The International Journal of Quantum Chemistry will >>> release a special >>> issue in connection with the workshop. Given the topic of the workshop >>> the special issue >>> will prioritize reviews, perspective articles, software tutorials and >>> documentation. >>> >>> ABOUT THE WORKSHOP: The workshop will address the challenge of >>> developing >>> maintainable, modular, modern, and scalable software dedicated to the >>> modeling of >>> environmental effects in Computational Molecular Sciences. >>> >>> ABOUT THE VENUE: the Coding Solvation Workshop will be >>> held from 23rd to the 25th of August 2017 (arrival on the 22nd and >>> departure on the 26th), and will take place at Hotel Universal >>> (http://www.livornohoteluniversal.com/en/) in Livorno, Italy. >>> >>> INVITED SPEAKERS: >>> Claudia Filippi (University of Twente, Netherlands) >>> Sebastian Hoefener (Karlsruhe Institute of Technology, Germany) >>> Harald Oberhofer (Technical University of Munich, Germany) >>> Giovanni Scalmani (Gaussian Inc., USA) >>> Lyudmila Slipchenko (Purdue University, USA) >>> Benjamin Stamm (RWTH Aachen University, Germany) >>> >>> Registration and abstract submission: >>> https://coding-solvation.gitlab.io/. >>> >>> The workshop is sponsored by the Molecular Sciences Software Institute >>> (http://molssi.org/) and is a satellite meeting to WATOC 2017 >>> (http://www.watoc2017.com/). >>> >>> We sincerely hope that you will join us in Livorno in August! >>> >>> Best wishes, >>> the organizing committee >>> >>> Oliviero Andreussi >>> Marco Caricato >>> Roberto Di Remigio >>> Luca Frediani >>> Heather Kulik >>> Filippo Lipparini >>> Benedetta Mennucci >>> Jogvan Magnus Olsen> >>> >>> --------------74E3837106F55DDA2B4949B5 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit

Dear Andreas,

it is indeed true the workshop does not feature anybody from the
COSMO-RS community among the keynote speakers, and I am sorry you feel
that COSMO has been left aside.

I am however surprised by your post: six months ago, when I had the idea
to organize the workshop, I sent you and many of our colleagues an email
asking if you were interested in either organizing or participating. You
clearly answered that you did not see how such a workshop "shall be
helpful to anybody".

I am glad to see that you changed your mind regarding the usefulness of
our workshop, and I can assure you that if you or anybody else from the
COSMO-RS community will subscribe and submit a relevant abstract, it
will be included in the program. As stated in my original post, there
are still spots available!

Best regards,
Luca Frediani

Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de]
What is a workshop on coding solvation worth, if it completely ignores
the currently most accurate solvation model, i.e. COSMO-RS.

Have fun with your workshop

Andreas


Am 12.05.2017 um 14:17 schrieb Luca Frediani luca.frediani()uit.no:

Sent to CCL by: "Luca  Frediani" [luca.frediani%a%uit.no]
Dear Colleague,

the registration for the "Coding solvation" workshop is still open, but
only a few spots are
still available at the venue hotel. Therefore, we strongly encourage
you to register soon.

CONTRIBUTED PRESENTATIONS: The deadline to submit an abstract for a
contributed
presentation has now been extended to the 15th of June.

IJQC SPECIAL ISSUE: The International Journal of Quantum Chemistry will
release a special
issue in connection with the workshop. Given the topic of the workshop
the special issue
will prioritize reviews, perspective articles, software tutorials and
documentation.

ABOUT THE WORKSHOP: The workshop will address the challenge of
developing
maintainable, modular, modern, and scalable software dedicated to the
modeling of
environmental effects in Computational Molecular Sciences.

ABOUT THE VENUE: the Coding Solvation Workshop will be
held from 23rd to the 25th of August 2017 (arrival on the 22nd and
departure on the 26th), and will take place at Hotel Universal
(http://www.livornohoteluniversal.com/en/) in Livorno, Italy.

INVITED SPEAKERS:
Claudia Filippi (University of Twente, Netherlands)
Sebastian Hoefener (Karlsruhe Institute of Technology, Germany)
Harald Oberhofer (Technical University of Munich, Germany)
Giovanni Scalmani (Gaussian Inc., USA)
Lyudmila Slipchenko (Purdue University, USA)
Benjamin Stamm (RWTH Aachen University, Germany)

Registration and abstract submission:
https://coding-solvation.gitlab.io/.

The workshop is sponsored by the Molecular Sciences Software Institute
(http://molssi.org/) and is a satellite meeting to WATOC 2017
(http://www.watoc2017.com/).

We sincerely hope that you will join us in Livorno in August!

Best wishes,
the organizing committee

Oliviero Andreussi
Marco Caricato
Roberto Di Remigio
Luca Frediani
Heather Kulik
Filippo Lipparini
Benedetta Mennucci
Jogvan Magnus Olsen>

--------------74E3837106F55DDA2B4949B5-- From owner-chemistry@ccl.net Sun May 14 13:46:00 2017 From: "Elvis Martis elvis_bcp[-]elvismartis.in" To: CCL Subject: CCL:G: Gaussian 09w to Autodock Message-Id: <-52803-170514053442-26217-rwCgoS2uS7D/6reAqoTKUA_+_server.ccl.net> X-Original-From: Elvis Martis Content-Type: multipart/alternative; boundary="f403045ea1fa908d5c054f78a59f" Date: Sun, 14 May 2017 15:04:15 +0530 MIME-Version: 1.0 Sent to CCL by: Elvis Martis [elvis_bcp]![elvismartis.in] --f403045ea1fa908d5c054f78a59f Content-Type: text/plain; charset="UTF-8" Hi, If you have access to Gaussview, you can save the optimised geometry as PDB or mol2 for autodock. Alternatively, you can use Maestro-GUI to load gauss outfile and save the PDB. For autodock you need to load pdb and then save it to pdbqt using MGL toots. Best Regards [image: photo] Elvis Martis Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in Skype. adrian_elvis12 On 14 May 2017 at 13:56, Partha Sengupta anapspsmo*gmail.com < owner-chemistry^_^ccl.net> wrote: > Friends, I want to do docking of a drug molecule to a protein in Autodock. > I a want to convert the Gaussian 09w file to Auutodock. But failed. I have > the cartesian coordinate data, is it possible to convert the cartesian data > to Autodock/ > partha > > -- > > > *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, > Burdwan* > --f403045ea1fa908d5c054f78a59f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi,

If you have access to Gaussview, you can save t= he optimised geometry as PDB or mol2 for autodock.

Alternatively, you= can use =C2=A0Maestro-GUI to load gauss outfile=C2=A0and save the PDB.

For autodock you need to load pdb and then save it to pdbqt=C2=A0using M= GL toots.

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0Best Regards=

Elvis Martis
Ph.D. Student (Computatio= nal Chemistry)
=C2=A0at=C2=A0= Bombay Col= lege of Pharmacy

A=C2=A0=C2=A0Kalina, Santacruz [E], Mumbai 400098, INDI= A
W=C2=A0www.elvismartis= .in

Skype.=C2=A0adrian_elvis12

<= /td>

<= /tbody>

<= a href=3D"http://www.linkedin.com/in/elvisadrianmartis/" style=3D"font-size= :11.0044px;background-color:rgb(26,117,208);color:rgb(0,191,232);text-decor= ation:none;line-height:23px;border-radius:50%;width:29px;height:23px;border= :0px;display:inline-block;text-align:center;padding-top:5px" target=3D"_bla= nk">

On 14 May 2017 at 13:56, Partha Sengupta ana= pspsmo*gmail.com <owner-chemistry^_^c= cl.net> wrote:

Friends, I want to do docking of a drug molecule to a protein in=C2=A0= Autodock. I a want to convert the Gaussian 09w file to Auutodock. But faile= d. I have the cartesian coordinate data, is it possible to convert the cart= esian data to Autodock/
= partha

--
Dr. Partha Sarathi= Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

--f403045ea1fa908d5c054f78a59f-- From owner-chemistry@ccl.net Sun May 14 14:21:00 2017 From: "Dr. Renjith Raveendran Pillai renjithkadavoor^_^gmail.com" To: CCL Subject: CCL:G: Gaussian 09w to Autodock Message-Id: <-52804-170514055700-31585-/XYqojuyb1l3PqPx4ZtpWw*|*server.ccl.net> X-Original-From: "Dr. Renjith Raveendran Pillai" Content-Type: multipart/alternative; boundary="94eb2c0877025f5d81054f78f5c3" Date: Sun, 14 May 2017 15:26:54 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Renjith Raveendran Pillai" [renjithkadavoor^^^gmail.com] --94eb2c0877025f5d81054f78f5c3 Content-Type: text/plain; charset="UTF-8" Dear Friend, You could use open babel, which is a free software for converting file formats. Regards On 14 May 2017 2:59 p.m., "Partha Sengupta anapspsmo*gmail.com" < owner-chemistry*o*ccl.net> wrote: > Friends, I want to do docking of a drug molecule to a protein in Autodock. > I a want to convert the Gaussian 09w file to Auutodock. But failed. I have > the cartesian coordinate data, is it possible to convert the cartesian data > to Autodock/ > partha > > -- > > > *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, > Burdwan* > --94eb2c0877025f5d81054f78f5c3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear Friend,

You could use open babel, w= hich is a free software for converting file formats.

Regards

On 14 May 2017 2:59 p.m., "Partha Sengupta anapspsmo*gmail.com" <owner-chemistry*o*ccl.net> wrote:

Friends, I want to do docking of= a drug molecule to a protein in=C2=A0Autodock. I a want to convert the Gau= ssian 09w file to Auutodock. But failed. I have the cartesian coordinate da= ta, is it possible to convert the cartesian data to Autodock/

partha

Dr. Partha Sarathi Sengupta<= br>Associate Professor
Vivekananda Mahavidyalaya, Burdwan=

--94eb2c0877025f5d81054f78f5c3--