From owner-chemistry@ccl.net Mon Jan 13 07:03:00 2014 From: "Krati Joshi kjjulie.joshi . gmail.com" To: CCL Subject: CCL: Error in SYMDEG while doing Bader charge analysis in deMon2k2.4.1 Message-Id: <-49542-140113070119-15494-ywNsWi38gWhfYzfdBAXTvA++server.ccl.net> X-Original-From: "Krati Joshi" Date: Mon, 13 Jan 2014 07:01:18 -0500 Sent to CCL by: "Krati Joshi" [kjjulie.joshi[-]gmail.com] Dear All, I am working on a planner graphene sheet with 24 carbon atoms. I am facing a problem while performing Bader charge analysis with deMon2k.2.4.1 code. All the time my calculations are terminating with the following error message: "ERROR IN SYMDEG" "Abnormal Program termination in SYMDEG" If anybody can suggest me something in this matter it will be highly obliged. Thanks in advance. From Krati Joshi CSIR-Central Electrochemical Research Institute, Karaikudi, India Email-kjjulie.joshi-at-gmail.com From owner-chemistry@ccl.net Mon Jan 13 09:35:01 2014 From: "Partha Sengupta anapspsmo=-=gmail.com" To: CCL Subject: CCL: molden Message-Id: <-49543-140112234331-377-KTa+wXsTtkkL+6MZjdIkGA^server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7b15ae41673e9704efd2b7f5 Date: Mon, 13 Jan 2014 10:13:25 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo=gmail.com] --047d7b15ae41673e9704efd2b7f5 Content-Type: text/plain; charset=ISO-8859-1 I dpwnload Molden. Then what to do to got the NBOand NLMO in this Molden.It will be beneficiary to me if the installation and working procedure be stated in sequentially. I have no idea about Fortran, Java, Unix and Linux system. Partha S Sengupta -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --047d7b15ae41673e9704efd2b7f5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I=A0 dpwnload Molden.
Then what to do to = got the NBOand NLMO in this Molden.It will=20 be beneficiary to me if the installation and working procedure be stated in sequentially.
I have no idea about Fortran, Java, Unix and Linux system.
P= artha S Sengupta=A0


--
Dr. Partha Sarathi Sengupta
Associate Profe= ssor
Vivekananda Mahavidyalaya, Burdwan
--047d7b15ae41673e9704efd2b7f5-- From owner-chemistry@ccl.net Mon Jan 13 10:10:00 2014 From: "sam paul reachsampaul===gmail.com" To: CCL Subject: CCL: HB/nonbonded interactions between ligand and protein using HBPLUS Message-Id: <-49544-140113093109-29749-4GyjGPRYmQSs2J3RR2gdPQ]~[server.ccl.net> X-Original-From: "sam paul" Date: Mon, 13 Jan 2014 09:31:08 -0500 Sent to CCL by: "sam paul" [reachsampaul|gmail.com] we have developed a flexible ligand - rigid receptor docking tool. The docking tool gives optimal structures of the ligand in .mol2 format and the receptor protein structure is in .pdb format. I kindly request suggestions/ideas to help me to find the hydrogen bond interactions and non- bonded interactions between the protein and the ligand using HBPLUS. Thank you. From owner-chemistry@ccl.net Mon Jan 13 11:10:00 2014 From: "Julio Dominguez acheron24 .. hotmail.com" To: CCL Subject: CCL: HB/nonbonded interactions between ligand and protein using HBPLUS Message-Id: <-49545-140113105509-24278-629wAeH+bBf9VN3zQ3siSQ(0)server.ccl.net> X-Original-From: Julio Dominguez Content-Type: multipart/alternative; boundary="_19283e2d-61a0-445b-a625-4889e7df1a7b_" Date: Mon, 13 Jan 2014 15:55:03 +0000 MIME-Version: 1.0 Sent to CCL by: Julio Dominguez [acheron24(!)hotmail.com] --_19283e2d-61a0-445b-a625-4889e7df1a7b_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Sam=2C=20 You need to convert the ligand from mol to pdb format and make it a single = file with your receptor pdb file. In fact=2C you need two files=2C at least= :receptor as a PDB and ligand+receptor as a PDB file. That way you can subs= tract the Hbonds present in the protein alone vs. those formed in the compl= ex. Cheers > From: owner-chemistry * ccl.net > To: acheron24 * hotmail.com > Subject: CCL: HB/nonbonded interactions between ligand and protein using = HBPLUS > Date: Mon=2C 13 Jan 2014 09:31:08 -0500 >=20 >=20 > Sent to CCL by: "sam paul" [reachsampaul|gmail.com] > we have developed a flexible ligand - rigid receptor docking tool. The=20 > docking tool gives optimal structures of the ligand in .mol2 format and t= he=20 > receptor protein structure is in .pdb format. I kindly request=20 > suggestions/ideas to help me to find the hydrogen bond interactions and = non- > bonded interactions between the protein and the ligand using HBPLUS. Than= k=20 > you. >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_19283e2d-61a0-445b-a625-4889e7df1a7b_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Sam=2C =3B

You need to convert the ligand from mol to pdb format and make it a singl= e file with your receptor pdb file. In fact=2C you need two files=2C at lea= st:
receptor as a PDB and ligand+receptor as a PDB file. That w= ay you can substract the Hbonds present in the protein alone vs. those form= ed in the complex.

Cheers
=

>=3B From: owner-chemistry * ccl.net
>=3B To: ache= ron24 * hotmail.com
>=3B Subject: CCL: HB/nonbonded interactions between= ligand and protein using HBPLUS
>=3B Date: Mon=2C 13 Jan 2014 09:31:0= 8 -0500
>=3B
>=3B
>=3B Sent to CCL by: "sam paul" [reachs= ampaul|gmail.com]
>=3B we have developed a flexible ligand - rigid rec= eptor docking tool. The
>=3B docking tool gives optimal structures o= f the ligand in .mol2 format and the
>=3B receptor protein structure = is in .pdb format. I kindly request
>=3B suggestions/ideas to help m= e to find the hydrogen bond interactions and non-
>=3B bonded interac= tions between the protein and the ligand using HBPLUS. Thank
>=3B you= .
>=3B
>=3B
>=3B
>=3B -=3D This is automatically add= ed to each message by the mailing script =3D-
>=3B To recover the emai= l address of the author of the message=2C please change
>=3B the stran= ge characters on the top line to the * sign. You can also
>=3B look up= the X-Original-From: line in the mail header.
>=3B
>=3B E-mail = to subscribers: CHEMISTRY * ccl.net or use:
>=3B http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message
>=3B
>=3B E-mail to administrator= s: CHEMISTRY-REQUEST * ccl.net or use
>=3B http://www.ccl.net/cgi-= bin/ccl/send_ccl_message
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&g= t=3B
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>= =3B Before posting=2C check wait time at: http://www.ccl.net
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>=3B Conferences: http://server.c= cl.net/chemistry/announcements/conferences/
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>=3B Search Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml
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>= =3B If your mail bounces from CCL with 5.7.1 error=2C check:
>=3B =
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>=3B RTFI: http://www.ccl= .net/chemistry/aboutccl/instructions/
>=3B
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=
= --_19283e2d-61a0-445b-a625-4889e7df1a7b_-- From owner-chemistry@ccl.net Mon Jan 13 12:14:01 2014 From: "Andreas H Goeller agoeller(0)live.de" To: CCL Subject: CCL:G: How to setup DFTB in Gaussian with dispersion correction? Message-Id: <-49546-140113120907-32327-pNs6EFR1Nlut+5kR8EOheA^^^server.ccl.net> X-Original-From: "Andreas H Goeller" Date: Mon, 13 Jan 2014 12:09:06 -0500 Sent to CCL by: "Andreas H Goeller" [agoeller###live.de] Dear CCL community, I want to use Gaussian 09 d1 to do DFTB calculations with Elstner parameter files and I want to apply dispersion corrections, in my case the BJ corrections as described by Grimme. (EmpiricalDispersion=GD3BJ) The manual explains how to set environment variables to give the respective parameters for S8 and the ABJ1 and ABJ2, like export GAUSS_DFTD3_S8=2375000 It works but is tedious in a queueing environment since it means that you have to modify your submit script to set these parameters at runtime if keywords are set. The big issue is that it becomes totally unfeasible for link jobs. Has anybody added the parameters to the source code? It is easy to find where to set them but I am not sure about the syntax and if that would be sufficient. Andreas From owner-chemistry@ccl.net Mon Jan 13 14:59:00 2014 From: "Patrizia Calaminici pcalamin-.-cinvestav.mx" To: CCL Subject: CCL: Error in SYMDEG while doing Bader charge analysis in deMon2k2.4.1 Message-Id: <-49547-140113145004-920-lxfzsBx4JtvRvjHsYVeXDg|-|server.ccl.net> X-Original-From: Patrizia Calaminici Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_ADB6DC46AB9A5F4EA8A097875C2190A227AA8DDECINVESTAVMB01ci_" Date: Mon, 13 Jan 2014 19:53:46 +0000 MIME-Version: 1.0 Sent to CCL by: Patrizia Calaminici [pcalamin*cinvestav.mx] --_000_ADB6DC46AB9A5F4EA8A097875C2190A227AA8DDECINVESTAVMB01ci_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL list members: For the report of deMon2k problems please email directly to speedy/./cinvestav.mx. As attachment provide your input and output file. Regards, The deMon developer team /./=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/./ Prof. Dr. Patrizia Calaminici Departamento de Quimica, CINVESTAV, Centro De Investigacion Y De Estudios Avanzados, Av. Instituto Politecnico Nacional, 2508 A.P. 14-740 Mexico D.F. 07000 MEXICO Tel: 5255-5-747-3911 (Office) 5255-5-747-3800 Ext. 4411, 4465 (Labs) Fax: 5255-5-747-3389 E-mails: pcalamin/./cinvestav.mx, calaminicipatrizia/./gmail.com http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminici= Patrizia.aspx Secretary: Miss. Lorena Sanchez Mendoza Tel: 5255-5-747-3800 Ext. 4408 E-mail: lsmendoza/./cinvestav.mx /./=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/./ > From: "Krati Joshi kjjulie.joshi . gmail.com" > Subject: CCL: Error in SYMDEG while doing Bader charge analysis in deMon2k2= .4.1 Date: January 13, 2014 1:01:18 PM GMT+01:00 To: "Malkin, Vladimir G. " > Reply-To: CCL Subscribers > Sent to CCL by: "Krati Joshi" [kjjulie.joshi[-]gmail.com= ] Dear All, I am working on a planner graphene sheet with 24 carbon atoms. I am facing = a problem while performing Bader charge analysis with deMon2k.2.4.1 code. A= ll the time my calculations are terminating with the following error messag= e: "ERROR IN SYMDEG" "Abnormal Program termination in SYMDEG" If anybody can suggest me something in this matter it will be highly oblige= d. Thanks in advance. > From Krati Joshi CSIR-Central Electrochemical Research Institute, Karaikudi, India Email-kjjulie.joshi-at-gmail.com -=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY/./ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_ADB6DC46AB9A5F4EA8A097875C2190A227AA8DDECINVESTAVMB01ci_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCL list members:

For the report of deMon2k problems please email directly to

speedy/./cinvestav.mx.

As attachment provide your input and output file.

Regards,

The deMon developer team

   
/./=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/./
    Prof. Dr. Patrizia= Calaminici
    Departamento de Quimica,
    CINVESTAV, Centro De Investigacion &n= bsp;       
    Y De Estudios Avanzados,     &n= bsp;            = ;  
    Av. Instituto Politecnico Nacional, 2508 &= nbsp; 
    A.P. 14-740 Mexico D.F. 07000     &n= bsp;       
    MEXICO 
   
    Tel: 5255-5-747-3911 (Office)    &nb= sp;         
         5255-5-747-3800 Ext. = 4411, 4465 (Labs) 
    Fax: 5255-5-747-3389       = ;            &n= bsp;   
    E-mails: pcalamin/./cinve= stav.mx,
&n= bsp;            calaminicipatrizia/./gmail.com 
    http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminiciPatr= izia.aspx

    Secretary: Miss. Lorena Sanchez Mendoza
    Tel: 5255-5-747-3800 Ext. 4408
    E-mail: lsmendoza/./cin= vestav.mx
/./=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/./
<= br>

From: "Krati Jo= shi kjjulie.joshi . gmail.com" <owner-chemistry/./cc= l.net>
Subject: <= /span>CCL: Err= or in SYMDEG while doing Bader charge analysis in deMon2k2.4.1
Date: January 13, 20= 14 1:01:18 PM GMT+01:00
To: "Malkin, Vl= adimir G. " <Vladimir.Malkin/./savba.sk>
Reply-To: = CCL Subscr= ibers <chemistry/./= ccl.net>


Sent to CCL by: "Krati  Joshi" [kjjulie.joshi[-]gmail.com]
Dear All,


I am working on a planner graphene sheet with 24 carbon atoms. I am facing = a problem while performing Bader charge analysis with deMon2k.2.4.1 code. A= ll the time my calculations are terminating with the following error messag= e:

"ERROR IN SYMDEG"
"Abnormal Program termination in SYMDEG"


If anybody can suggest me something in this matter it will be highly oblige= d. Thanks in advance.

> From
Krati Joshi
CSIR-Central Electrochemical Research Institute, Karaikudi, India
Email= -kjjulie.joshi-at-gmail.com



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