From owner-chemistry@ccl.net Sat Oct 1 01:35:01 2011 From: "rocky walden rocky.walden19=gmail.com" To: CCL Subject: CCL: AUTODOCK error Message-Id: <-45562-111001013155-14142-g7WTb10I1FsHW3lhlCiDQQ,server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016e64ea93e47d02504ae360e16 Date: Sat, 1 Oct 2011 11:01:37 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19|,|gmail.com] --0016e64ea93e47d02504ae360e16 Content-Type: text/plain; charset=ISO-8859-1 Hi Sola, I am afraid that Autodock could not handle Metal-atoms. As far as I know that since AutoDock doesn't handle metal atoms so parameters for 'Metal atoms' is not available or parametrization is not done. Please correct me if I am wrong. Thanks Rocky On Thu, Sep 29, 2011 at 3:20 PM, rv sola rvsolo(!)gmail.com < owner-chemistry+/-ccl.net> wrote: > > Sent to CCL by: "rv sola" [rvsolo]![gmail.com] > dear ccl members, > > i would like to dock a metal complex with DNA. i am using > AUTODOCK windows version and i got the following error message while > processing the docking. > > ERROR: Unknown ligand atom type "Cu"; add parameters for it to the > parameter library first! > > if anybody experienced the same problem and possible solution? > > yours, > > rv sola> > > --0016e64ea93e47d02504ae360e16 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sola,

=A0=A0=A0=A0 I am afraid that Autodock could not handle Met= al-atoms.
=A0=A0=A0=A0 As far as I know that since AutoDock doesn't = handle metal atoms so parameters for 'Metal atoms' is not available= or parametrization is not done.

=A0=A0=A0 Please correct me if I am wrong.
Thanks
Rocky

On Thu, Sep 29, 2011 at 3:20 PM, rv sola rvsolo(!)= gmail.com <owner-chemistry+/-ccl.net> wro= te:

Sent to CCL by: "rv =A0sola" [rvsolo]![gmail.com]
dear ccl members,

=A0 =A0 =A0 =A0 =A0 =A0i would like to dock a metal complex with DNA. i am= using AUTODOCK windows version and i got the following error message while= processing the docking.

ERROR: =A0Unknown ligand atom type "Cu"; add parameters for it to= the parameter library first!

if anybody experienced the same problem and possible solution?

yours,

rv sola



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--0016e64ea93e47d02504ae360e16-- From owner-chemistry@ccl.net Sat Oct 1 05:57:01 2011 From: "Sanjay Bharathwaj computationalchemist : gmail.com" To: CCL Subject: CCL: X-Ray diffraction Message-Id: <-45563-111001055344-9691-Czqsf6f/SsQTULyy08p/Mg(0)server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=bcaec520ee7729fbe204ae39b7c4 Date: Sat, 1 Oct 2011 11:53:36 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist**gmail.com] --bcaec520ee7729fbe204ae39b7c4 Content-Type: text/plain; charset=ISO-8859-1 Dear Folks, I have X-ray diffraction pattern for different samples both simulated and experimentally obtained. The sample contain three different element both heavy (Mo/Co) and light (say Carbon, Oxygen) For these samples, I observe two major peaks in experiments while i have more number of peaks in theory. I would attribute it to the fact that the peaks corresponds to the light element in the sample, are not reflected in experimental spectrum. But, however, i wanted to know how the peaks obtained in x-ray diffraction could be assigned to the individual bonds in the sample. I am looking for literature/Tutorials/Suggestions > from you and i thank you in advance. If you need more details about this please let me know and i look forward hearing from you. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --bcaec520ee7729fbe204ae39b7c4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Folks,

I have X-ray diffraction pattern for dif= ferent samples
both simulated and experimentally obtained.
The sample conta= in three different element both
heavy (Mo/Co) and light (say Carb= on, Oxygen)

For these samples,=A0I observe two maj= or peaks in experiments while
i have more number of peaks in theory.

I woul= d attribute it to the fact that the peaks
corresponds to the ligh= t element in the sample,
are not reflected in experimental spectr= um.=A0

But, however, i wanted to know how the
peaks = obtained in x-ray diffraction could be
assigned to the individual= bonds in the sample.

I am looking for literature/= Tutorials/Suggestions
from you and i thank you in advance.

If you n= eed more details about this please let me know
and i look forward= hearing from you.

Sanjay


--
Regards,
Dr. Sanjay Bharathwaj Kumar,=
Dharmendra Institute of Technology,
India.
--bcaec520ee7729fbe204ae39b7c4--