From owner-chemistry@ccl.net Wed Mar 8 02:14:00 2017 From: "teja reddy reddyteja80^_^gmail.com" To: CCL Subject: CCL: Gaussian error Message-Id: <-52668-170308021132-20657-7FunEzmoobGl7PX5zUcN/Q+*+server.ccl.net> X-Original-From: teja reddy Content-Type: multipart/alternative; boundary=94eb2c18fe7838d30e054a32d647 Date: Wed, 8 Mar 2017 12:41:26 +0530 MIME-Version: 1.0 Sent to CCL by: teja reddy [reddyteja80+*+gmail.com] --94eb2c18fe7838d30e054a32d647 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable =E2=80=8BDear Friends, I am using gaussin 09 (32-bit bineries) and optimizing a molecule starting > from crystal geometry. The following error hasbeen observed. Is this error due to memory limit? please comment, thanks in advance. Number 998 Base 20495 End 20695 End1 20695 Wr Pntr 20495 Rd Pntr 20495 Length 200 dumping /fiocom/, unit =3D 3 NFiles =3D 1 SizExt =3D 524288 WInBlk = =3D 512 defal =3D T LstWrd =3D 67072 FType=3D2 FMxFil=3D10= 000 Number 0 Base 20480 End 67072 End1 67072 Wr Pntr 20480 Rd Pntr 20480 Length 46592 Error termination in NtrErr: NtrErr called from FIOCnC. =E2=80=8B --=20 *Venkata Pera Reddy B.* *Research scholar* *Department of Chemistry* *National Institute of Technology* *Durgapur**-713209, W.B, India* *vprb.15cy1101 . phd.nitdgp.ac.in * *reddyteja80 . gmail.com * *https://scholar.google.co.in/citations?hl=3Den&user=3Dkn1nFj4AAAAJ * *https://www.researchgate.net/profile/Venkata_Reddy_B * --94eb2c18fe7838d30e054a32d647 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
=E2=80=8BDear Friends,=C2=A0
I am using gaussin 09 (32-bit bineries) and optimizi= ng a molecule starting from crystal geometry. The following error hasbeen o= bserved. Is this error due to memory limit? please comment, thanks in advan= ce.

=

=C2=A0Number =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0998
=C2=A0Base =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020495=
=C2=A0End= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 20695
=C2=A0End1 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A020695
=C2=A0Wr Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20495
=C2=A0Rd Pntr =C2=A0 =C2= =A0 =C2=A0 =C2=A0 20495
=C2=A0Length =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0200


<= div class=3D"gmail_default">=C2=A0dumping /fiocom/,= unit =3D 3 NFiles =3D =C2=A0 =C2=A0 1 SizExt =3D =C2=A0 =C2=A0524288 WInBl= k =3D =C2=A0 =C2=A0 =C2=A0 512
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0defal =3D T LstWrd =3D =C2=A0 =C2=A0 =C2=A0 67072 FType=3D= 2 FMxFil=3D10000

=C2=A0Number =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00
=C2=A0Base =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020480
=C2=A0End =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 67072
=C2=A0End1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A067072
=C2=A0Wr Pntr =C2=A0 =C2= =A0 =C2=A0 =C2=A0 20480
=C2=A0Rd Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20480
<= div class=3D"gmail_default">=C2=A0Length =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A046592
=C2=A0Error termination in NtrErr:
=C2=A0NtrErr called from FIOCn= C.
=E2= =80=8B

--
=
Venkata = Pera Reddy B.
Research scholar<= /i>
Department of Chemistr= y
National Institute of Technolo= gy
Durgapur-713209, W.B, India




--94eb2c18fe7838d30e054a32d647-- From owner-chemistry@ccl.net Wed Mar 8 09:19:00 2017 From: "Rangsiman Ketkaew rangsiman1993#%#gmail.com" To: CCL Subject: CCL: Gaussian error Message-Id: <-52669-170308033823-345-6Mj04FZzRYxIeYJsYOQxXw*server.ccl.net> X-Original-From: Rangsiman Ketkaew Content-Type: multipart/alternative; boundary=001a1134f062be6c16054a340cd6 Date: Wed, 8 Mar 2017 15:38:15 +0700 MIME-Version: 1.0 Sent to CCL by: Rangsiman Ketkaew [rangsiman1993^^gmail.com] --001a1134f062be6c16054a340cd6 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Could you post your input file officially ? Rangsiman - - - Rangsiman Ketkaew =E2=9C=89 rangsiman1993|,|gmail.com =E2=9C=89 rangsiman_k|,|sci.tu.ac.th website https://sites.google.com/site/compchem403/ On 8 Mar 2017 9:15 a.m., "teja reddy reddyteja80^_^gmail.com" < owner-chemistry|,|ccl.net> wrote: > > =E2=80=8BDear Friends, > I am using gaussin 09 (32-bit bineries) and optimizing a molecule startin= g > from crystal geometry. The following error hasbeen observed. Is this erro= r > due to memory limit? please comment, thanks in advance. > > > Number 998 > Base 20495 > End 20695 > End1 20695 > Wr Pntr 20495 > Rd Pntr 20495 > Length 200 > > > dumping /fiocom/, unit =3D 3 NFiles =3D 1 SizExt =3D 524288 WInBl= k =3D > 512 > defal =3D T LstWrd =3D 67072 FType=3D2 FMxFil=3D= 10000 > > Number 0 > Base 20480 > End 67072 > End1 67072 > Wr Pntr 20480 > Rd Pntr 20480 > Length 46592 > Error termination in NtrErr: > NtrErr called from FIOCnC. > =E2=80=8B > > -- > *Venkata Pera Reddy B.* > *Research scholar* > *Department of Chemistry* > *National Institute of Technology* > *Durgapur**-713209, W.B, India* > *vprb.15cy1101---phd.nitdgp.ac.in * > *reddyteja80---gmail.com * > > *https://scholar.google.co.in/citations?hl=3Den&user=3Dkn1nFj4AAAAJ > * > > *https://www.researchgate.net/profile/Venkata_Reddy_B > * > > > > > --001a1134f062be6c16054a340cd6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Could you post your input file officially ?

Rangsiman



- - -
Rangsiman Ketkaew

=E2=9C= =89=C2=A0rangsiman1993|,|gmail.com= =C2=A0
=E2=9C=89=C2=A0ra= ngsiman_k|,|sci.tu.ac.th
website=C2=A0https://sites.google.com/site/compchem403/
= =C2=A0=C2=A0=C2=A0

On 8 Mar 2017 9:15 a.m., "teja reddy reddyteja80^_= ^gmail.com" <owner-chemistry|,|ccl.net> wrote:

=E2=80=8BDear Friends,=C2= =A0
I am using= gaussin 09 (32-bit bineries) and optimizing a molecule starting from cryst= al geometry. The following error hasbeen observed. Is this error due to mem= ory limit? please comment, thanks in advance.


=C2=A0Number =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0998
=C2=A0Base =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020495
=C2=A0End =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 20695
=C2=A0End1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020695
=C2=A0Wr Pntr =C2=A0= =C2=A0 =C2=A0 =C2=A0 20495
=C2=A0Rd Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20495
=C2=A0Length =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0200

=
=C2=A0dumping /fiocom/, unit =3D 3 NFiles =3D =C2=A0 =C2= =A0 1 SizExt =3D =C2=A0 =C2=A0524288 WInBlk =3D =C2=A0 =C2=A0 =C2=A0 512
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0defal =3D T LstW= rd =3D =C2=A0 =C2=A0 =C2=A0 67072 FType=3D2 FMxFil=3D10000

=C2=A0Number =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00
<= font color=3D"#000000">=C2=A0Base =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 20480
=C2= =A0End =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 67072
=C2=A0End1 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A067072
=C2=A0Wr Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20480<= /div>
=C2=A0Rd Pntr =C2= =A0 =C2=A0 =C2=A0 =C2=A0 20480
=C2=A0Length =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A046592
=C2=A0Error= termination in NtrErr:
=C2=A0NtrErr called from FIOCnC.
=E2=80=8B

--
<= div dir=3D"ltr">
Venkata Pera Reddy = B.
Research scholar
Department of Chemistry
National Institute of Technology




--001a1134f062be6c16054a340cd6-- From owner-chemistry@ccl.net Wed Mar 8 09:54:00 2017 From: "Subrata Dasgupta dasguptasubrata02*|*gmail.com" To: CCL Subject: CCL: Parameterization of Pt in Autodock Vina Message-Id: <-52670-170308045504-6891-GecD1Y64ROHk456faDOk7w ~ server.ccl.net> X-Original-From: Subrata Dasgupta Content-Type: multipart/alternative; boundary=001a1140443cfca47d054a351ebb Date: Wed, 8 Mar 2017 15:24:56 +0530 MIME-Version: 1.0 Sent to CCL by: Subrata Dasgupta [dasguptasubrata02(0)gmail.com] --001a1140443cfca47d054a351ebb Content-Type: text/plain; charset=UTF-8 Dear friends, I am working with metal complexes and want to study the interaction of metal complexes in different proteins by docking methods. When i use auto-dock vina for my complexes i get an error that the Platinum is unparameterized. Please give some suggestions for Platinum parameterization. And how can i add parameters for Platinum. Please comment.. Thank you -- Subrata Dasgupta Dept. of Chemistry NIT Durgapur --001a1140443cfca47d054a351ebb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear friends,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 I am working with metal complexes and want to stud= y the interaction of metal complexes in different proteins by docking metho= ds. When i use auto-dock vina for my complexes i get an error that the Plat= inum is unparameterized. Please give some suggestions for Platinum paramete= rization. And how can i add parameters for Platinum. Please comment.. Thank= you=C2=A0

--
Subrata Dasgupta<= div>Dept. of Chemistry
NIT Durgapur
--001a1140443cfca47d054a351ebb-- From owner-chemistry@ccl.net Wed Mar 8 11:29:01 2017 From: "Morad El-Hendawy morad.elhendawy###yahoo.com" To: CCL Subject: CCL: Gaussian error Message-Id: <-52671-170308102333-8418-98q/7nUWLL23DqjlRo4bnA/./server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="----=_Part_2268621_1045695291.1488986604390" Date: Wed, 8 Mar 2017 15:23:24 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [morad.elhendawy!^!yahoo.com] ------=_Part_2268621_1045695291.1488986604390 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable =C2=A0Dear Venkata,The error is originated typically when you retrieve some= info from the checkpoint file such as guess, geometry, ...etc and these ar= e not included either because:1- You did not calculate them previously or 2- You=C2=A0 ran a freq job (for instance) and=C2=A0 the OPT job has not fi= nished yet=C2=A0 then the info needed weren't written to the checkpoint fil= e. In your case you may restart the job again recalling the guess and geome= try, then get this error. Therefore, start again with xyz coordinates.=C2= =A0=20 Sincerely,=C2=A0Morad M. El-Hendawy (Ph.D.)Assistant Professor of Physical = Chemistry Chemistry Department, Faculty of Science,Assiut University, New Vally Campu= s, EGYPT Tel: +2 01024408662; Fax: +2 0927925393 =20 On Wednesday, 8 March 2017, 17:18:51, teja reddy reddyteja80^_^gmail.co= m wrote: =20 =20 =E2=80=8BDear Friends,=C2=A0I am using gaussin 09 (32-bit bineries) and opt= imizing a molecule starting from crystal geometry. The following error hasb= een observed. Is this error due to memory limit? please comment, thanks in = advance. =C2=A0Number =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0998=C2=A0Base =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020495=C2=A0End =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 20695=C2=A0End1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= 20695=C2=A0Wr Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20495=C2=A0Rd Pntr =C2=A0 = =C2=A0 =C2=A0 =C2=A0 20495=C2=A0Length =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0200 =C2=A0dumping /fiocom/, unit =3D 3 NFiles =3D =C2=A0 =C2=A0 1 SizExt =3D = =C2=A0 =C2=A0524288 WInBlk =3D =C2=A0 =C2=A0 =C2=A0 512=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0defal =3D T LstWrd =3D =C2= =A0 =C2=A0 =C2=A0 67072 FType=3D2 FMxFil=3D10000 =C2=A0Number =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00=C2=A0Base = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A020480=C2=A0End =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 67072=C2=A0End1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A067072=C2=A0Wr Pntr =C2=A0 =C2=A0 =C2=A0 =C2=A0 20480=C2=A0Rd Pntr = =C2=A0 =C2=A0 =C2=A0 =C2=A0 20480=C2=A0Length =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A046592=C2=A0Error termination in NtrErr:=C2=A0NtrErr called from FIOCn= C.=E2=80=8B --=20 Venkata Pera Reddy B. Research scholarDepartment of ChemistryNational Institute of TechnologyDurg= apur-713209, W.B, Indiavprb.15cy1101---phd.nitdgp.ac.in reddyteja80---gmail.comhttps://scholar.google.co.in/citations?hl=3Den&user= =3Dkn1nFj4AAAAJ https://www.researchgate.net/profile/Venkata_Reddy_B =20 ------=_Part_2268621_1045695291.1488986604390 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
 = Dear Venkata,
The error is originated typically when you retrieve some info from the checkpoint file= such as guess= , geometry, ...etc and these are not included either because:=
1- You did not calculate them previ= ously or
2- You  ran a freq job (for i= nstance) and  the OPT job has not finished yet  then the info needed weren't written to the checkpoint fi= le. I= n your case you may restart the job again recalling the guess and geometry,= then get this error. Therefore,= start again with xyz coordinates. 
Sin= cerely, 
Morad M= . El-Hendawy (Ph.D.)
Assistant Professor of Physical Chemistry
Chemistry Departmen= t, Faculty of Science,
Assiut University, New Vally Campus, EGY= PT
Tel: +2 01024408662; Fax: +2 0927925393
<= div class=3D"qtdSeparateBR" id=3D"yui_3_16_0_ym19_1_1488975485149_18498">
On Wednesday, 8 March 2017, 17:18:51, teja reddy reddyteja= 80^_^gmail.com <owner-chemistry++ccl.net> wrote:


=E2=80=8BDear Friends, 
I am using gaussin 09 (32-bit bineries) and optimizi= ng a molecule starting from crystal geometry. The following error hasbeen o= bserved. Is this error due to memory limit? please comment, thanks in advan= ce.


 = ;Number            998
&nbs= p;Base            20495
 End           &nb= sp; 20695
 End1  =          20695
 Wr Pntr     &nb= sp;   20495
 Rd= Pntr         20495
 Length      = ;      200
<= br>

 dumping /fiocom/, unit =3D 3 NFiles =3D=     1 SizExt =3D    524288 WInBlk =3D     &n= bsp; 512
                 =  defal =3D T LstWrd =3D       67072 FType=3D2 FMxFil= =3D10000

<= div class=3D"yiv2009716503gmail_default" id=3D"yui_3_16_0_ym19_1_1488975485= 149_18774"> Number        =      0
&nbs= p;Base            20480
 End           &nb= sp; 67072
 End1           &= nbsp;67072
 Wr Pntr         2048= 0
 Rd Pntr   &nbs= p;     20480
 Length       =    46592
 Er= ror termination in NtrErr:
 NtrErr called from FIOCn= C.
=E2=80=8B

<= /div>--
Venkata Pera Reddy B.
Research scholar<= /b>
Department of Chemistry=
<= b id=3D"yui_3_16_0_ym19_1_1488975485149_29969">National Institute of Technology
<= div dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1488975485149_19076">Durgapur-713209, W.B, India


------=_Part_2268621_1045695291.1488986604390-- From owner-chemistry@ccl.net Wed Mar 8 12:04:00 2017 From: "Felipe Pineda pideca55 .. gmail.com" To: CCL Subject: CCL: Parameterization of Pt in Autodock Vina Message-Id: <-52672-170308114011-11547-XUQEXHVlfzNF6nv+aLCCkQ]_[server.ccl.net> X-Original-From: Felipe Pineda Content-Type: multipart/alternative; boundary=001a114cc7aed304b8054a3ac77e Date: Wed, 8 Mar 2017 17:40:04 +0100 MIME-Version: 1.0 Sent to CCL by: Felipe Pineda [pideca55*o*gmail.com] --001a114cc7aed304b8054a3ac77e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, study the literature, think yourself and do not expect someone else does that for you, as that it is maybe usual in "incredible" India. +-----------------------------------+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist | | Hotel Asystencki Nr. 2 | | Al. Gen. J. Hallera 241, R. 411 | | *PL-80 502 **Gda=C5=84sk* | | Polska - Poland | | Mobile: ++48-697-433629 | | E-Mail: pideca__hotmail.com | +-----------------------------------+ On Wed, Mar 8, 2017 at 10:54 AM, Subrata Dasgupta dasguptasubrata02*|* gmail.com wrote: > Dear friends, > I am working with metal complexes and want to study the > interaction of metal complexes in different proteins by docking methods. > When i use auto-dock vina for my complexes i get an error that the Platin= um > is unparameterized. Please give some suggestions for Platinum > parameterization. And how can i add parameters for Platinum. Please > comment.. Thank you > > -- > Subrata Dasgupta > Dept. of Chemistry > NIT Durgapur > --001a114cc7aed304b8054a3ac77e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,
study the literature, think yourself and= do not expect someone else does that for you, as that it is maybe usual in= "incredible" India.

+-----------------------------------+
| Luis Felipe Pineda De Castro, PhD |
| Computational=20 Chemist =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 |
| Hotel Asystencki Nr. 2=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 |
| Al. Gen. J. Hallera 241, R. = 411 =C2=A0 |
| PL-80 502 Gda=C5=84sk =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 |
| Polska - Poland= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 |
| Mobile: ++48-697-433629=C2=A0 =C2=A0=C2=A0=C2=A0 = =C2=A0 =C2=A0=C2=A0 |
| E-Mail: pideca__hot= mail.com=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 |
+-------------------= ----------------+

On Wed, Mar 8, 2017 at 10:54 AM, Subrata Das= gupta dasguptasubrata02*|*gmail.com <owner-chemistry__ccl.net> wrote:
Dear friends,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 I am working with metal complexes and want = to study the interaction of metal complexes in different proteins by dockin= g methods. When i use auto-dock vina for my complexes i get an error that t= he Platinum is unparameterized. Please give some suggestions for Platinum p= arameterization. And how can i add parameters for Platinum. Please comment.= . Thank you=C2=A0

--
Subrata Dasgup= ta
Dept. of Chemistry
NIT Durgapur

--001a114cc7aed304b8054a3ac77e-- From owner-chemistry@ccl.net Wed Mar 8 12:42:01 2017 From: "Ahmed Saeed ahmed_said5899**yahoo.com" To: CCL Subject: CCL:G: How to draw DOS and band structure from Gaussian 09 results? Message-Id: <-52673-170308123935-10418-8ygtl/6z+5p/6aHM3afVfA^_^server.ccl.net> X-Original-From: "Ahmed Saeed" Date: Wed, 8 Mar 2017 12:39:33 -0500 Sent to CCL by: "Ahmed Saeed" [ahmed_said5899##yahoo.com] Dear friends, I am studying electron transfer and electrical properties of a conductor using DFT calculations. I want to plot the DOS and the band structure of it using Gaussian 09 results. Is this possible? And if it is possible, what are the detailed procedures please? Thank you all. Ahmed From owner-chemistry@ccl.net Wed Mar 8 14:00:00 2017 From: "Herbert Fruchtl herbert.fruchtl+/-st-andrews.ac.uk" To: CCL Subject: CCL: Parameterization of Pt in Autodock Vina Message-Id: <-52674-170308135845-20911-KqkMc6H0HIs0GY98wQK4yw=server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 8 Mar 2017 19:00:10 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl[-]st-andrews.ac.uk] Dear Luis, This is a forum where people of different backgrounds and levels of theoretical knowledge ask for help. If you want to help them, you reply. If you don't, you don't. It's also not the place to air your prejudices against complete nations and automatically apply them to an individual asking for help. Sadly I have no experience with Autodock. Herbert On 08/03/17 16:40, Felipe Pineda pideca55 .. gmail.com wrote: > Hi, > study the literature, think yourself and do not expect someone else does that > for you, as that it is maybe usual in "incredible" India. > > +-----------------------------------+ > | Luis Felipe Pineda De Castro, PhD | > | Computational Chemist | > | Hotel Asystencki Nr. 2 | > | Al. Gen. J. Hallera 241, R. 411 | > | _PL-80 502 __GdaĹ„sk_ | > | Polska - Poland | > | Mobile: ++48-697-433629 | > | E-Mail: pideca-x-hotmail.com | > +-----------------------------------+ > > On Wed, Mar 8, 2017 at 10:54 AM, Subrata Dasgupta dasguptasubrata02*|*gmail.com > > wrote: > > Dear friends, > I am working with metal complexes and want to study the > interaction of metal complexes in different proteins by docking methods. > When i use auto-dock vina for my complexes i get an error that the Platinum > is unparameterized. Please give some suggestions for Platinum > parameterization. And how can i add parameters for Platinum. Please > comment.. Thank you > > -- > Subrata Dasgupta > Dept. of Chemistry > NIT Durgapur > > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed Mar 8 14:35:01 2017 From: "HALIM MOHAMMAD ABDUL mohammad-abdul.halim_-_univ-lyon1.fr" To: CCL Subject: CCL: Parameterization of Pt in Autodock Vina Message-Id: <-52675-170308135007-17204-K0H6fmH09svLzZmAjboa7w+/-server.ccl.net> X-Original-From: HALIM MOHAMMAD ABDUL Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Wed, 8 Mar 2017 18:49:58 +0000 MIME-Version: 1.0 Sent to CCL by: HALIM MOHAMMAD ABDUL [mohammad-abdul.halim===univ-lyon1.fr] Dear Subrata Dasgupta, The force field used in in Vina is not parameterized for Pt and other metals, you can take the force field and insert information for Pt which would be little taught if you are new to docking. You may also use other docking program such as Patchdock which is compatible with Pt metal. You may see this link for more information: http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Scientific%20Questions thanks, Mohammad Abdul HALIM Doctorant ILM, CNRS et Universit¨¦ Lyon 1 Institut Lumi¨¨re Mati¨¨re, Equipe: SpectroBio Cit¨¦ Lyonnaise de l'Environnement et de l'Analyse 5 rue de la Doua, 69100 Villeurbanne, France T¨¦l¨¦phone +33(0)4.72.44.58.75 ________________________________________ > From: owner-chemistry+mohammad-abdul.halim==univ-lyon1.fr _ ccl.net [owner-chemistry+mohammad-abdul.halim==univ-lyon1.fr _ ccl.net] on behalf of Felipe Pineda pideca55 .. gmail.com [owner-chemistry _ ccl.net] Sent: Wednesday, March 8, 2017 5:40 PM To: HALIM MOHAMMAD ABDUL Subject: CCL: Parameterization of Pt in Autodock Vina Hi, study the literature, think yourself and do not expect someone else does that for you, as that it is maybe usual in "incredible" India. +-----------------------------------+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist | | Hotel Asystencki Nr. 2 | | Al. Gen. J. Hallera 241, R. 411 | | PL-80 502 Gda¨˝sk | | Polska - Poland | | Mobile: ++48-697-433629 | | E-Mail: pideca-x-hotmail.com | +-----------------------------------+ On Wed, Mar 8, 2017 at 10:54 AM, Subrata Dasgupta dasguptasubrata02*|*gmail.com > wrote: Dear friends, I am working with metal complexes and want to study the interaction of metal complexes in different proteins by docking methods. When i use auto-dock vina for my complexes i get an error that the Platinum is unparameterized. Please give some suggestions for Platinum parameterization. And how can i add parameters for Platinum. Please comment.. Thank you -- Subrata Dasgupta Dept. of Chemistry NIT Durgapur From owner-chemistry@ccl.net Wed Mar 8 15:10:01 2017 From: "Edward Brothers chicoraed .. gmail.com" To: CCL Subject: CCL:G: How to draw DOS and band structure from Gaussian 09 results? Message-Id: <-52676-170308150551-28217-Leig7+kJMImE33FdM0VFwg^^server.ccl.net> X-Original-From: Edward Brothers Content-Type: multipart/alternative; boundary=94eb2c0d56cc60fe5e054a3da727 Date: Wed, 8 Mar 2017 23:05:44 +0300 MIME-Version: 1.0 Sent to CCL by: Edward Brothers [chicoraed**gmail.com] --94eb2c0d56cc60fe5e054a3da727 Content-Type: text/plain; charset=UTF-8 For a periodic system? See http://scuseria.rice.edu/gau/PBC-Guide.pdf Ed. On Wed, Mar 8, 2017 at 8:39 PM, Ahmed Saeed ahmed_said5899**yahoo.com < owner-chemistry]-[ccl.net> wrote: > > Sent to CCL by: "Ahmed Saeed" [ahmed_said5899##yahoo.com] > Dear friends, > > I am studying electron transfer and electrical > properties of a conductor using DFT calculations. I > want to plot the DOS and the band structure of it > using Gaussian 09 results. Is this possible? And if it > is possible, what are the detailed procedures please? > Thank you all. > > Ahmed> > > --94eb2c0d56cc60fe5e054a3da727 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
For a periodic =C2=A0system?=C2=A0 See=C2=A0http://scuseria.rice.edu/gau/PBC-G= uide.pdf

Ed.
<= br>
On Wed, Mar 8, 2017 at 8:39 PM, Ahmed Saeed a= hmed_said5899**yahoo.com <owner-che= mistry]-[ccl.net> wrote:

Sent to CCL by: "Ahmed=C2=A0 Saeed" [ahmed_said5899##yahoo.com]
Dear friends,

I am studying electron transfer and electrical
properties of a conductor using DFT calculations. I
want to plot the DOS and the band structure of it
using Gaussian 09 results. Is this possible? And if it
is possible, what are the detailed procedures please?
Thank you all.

Ahmed



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