[ADF-LIST] Export data from material studio to ADF package

نها احمد حسن احمد وزان nwazzan at kau.edu.sa
Tue Oct 17 12:08:35 CEST 2017

Dear Fedor,

Thank you very much for your email.

The video is very helpful.

However, when I run the job, it seems that the job is not running and the
output file is an empty one!?

Here is a screenshot:

[image: Inline image 1]

Could you please advise me about this topic.

Thanks,



On Mon, Oct 16, 2017 at 12:43 AM, Fedor Goumans <goumans at scm.com> wrote:

> Dear Nuha,
> See also this video at 19.25” where I demonstrate how to do this for a
> naphthalene cif file:
> https://www.scm.com/wp-content/uploads/MaterialsModeling.mp4#t=1164
>
> Best wishes,
> Fedor
>
> On 15 Oct 2017, at 07:56, Fedor Goumans <goumans at scm.com> wrote:
>
> Dear Nuha,
>
> If you have a cif or pdb with periodic boundary conditions, you could just
> import that in ADFinput, it should go to BAND to deal with periodicity.
> Then you probably want to make a supercell, go to ADF (0 periodicity) and
> just select the two molecules you are interested in.
>
> See also: https://www.scm.com/adf-modeling-suite/wizard/organic-
> electronics/electron-and-hole-mobilities-in-organic-electronics/
>
> If the cif or pdb is not properly saved by Materials Studio, there may be
> some problems importing it. Could you send it to support at scm.com ?
>
> Best wishes,
> Fedor
>
> On 14 Oct 2017, at 14:40, ⁨نها احمد حسن احمد وزان⁩ <⁨nwazzan at kau.edu.sa⁩>
> wrote:
>
> Good morning,
>
> I have this question please:
>
> I have run a calculation using the polymorph predictor module in
> Materials Studio 5.5 program to predict the crystal structure of designed
> hole transporting materials. I have got a frame represents the most stable
> crystal structure of the minimum energy like the one represented in the
> picture below:
>
> <image.png>
>
> Now with a cell that has two molecules, I want to calculate the charge
> transfer integral between the two molecules using the ADF package.
>
> But, I do not know how to open the .xsd file in the material studio in the
> ADF?
>
> I have tried to export the file in different extension such as .mol2,
> .pdb, .cif but I have distorted molecular structure!
>
> Could you please advise me about this topic.
>
> Regards,
> Nuha
>
> Note: I am a new user of the ADF package
>
>
> --
> Dr. Nuha Wazzan
> Associate Professor of Physical Chemistry
>
> School of Chemistry
> King Abdulaziz University
> P.O Box 42805
> Jeddah 21551
> Saudi Arabia
>
> e-mail: nwazzan at kau.edu.sa
>
> Disclaimer: The information contained in this message is intended for the
> addressee only and may contain classified information. If you are not the
> addressee, please delete this message and notify the sender; you should not
> copy or distribute this message or disclose its contents to anyone. Any
> views or opinions expressed in this message are those of the individual(s)
> and not necessarily of the university. No reliance may be placed on this
> message without written confirmation from an authorized representative of
> its contents. No guarantee is implied that this message or any attachment
> is virus free or has not been intercepted and amended.
>
> إخلاء مسؤليه:  ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم،
> وربما تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة
> واشعار المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين.
> ويجدر بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية
> وليست بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم
> تحصل على موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه
> الرسالة أو مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها
>
> _______________________________________________
> ADFlist mailing list
> ADFlist at scm.com
> https://lists.scm.com/mailman/listinfo/adflist
>
>
> Dr. T. P. M. (Fedor) Goumans
> Business Developer
> Software for Chemistry & Materials
> Vrije Universiteit, FEW, Theoretical Chemistry
> De Boelelaan 1083
> 1081 HV Amsterdam, The Netherlands
> T +31 20 598 7625
> https://www.scm.com
> https://twitter.com/SCM_Amsterdam
> https://www.linkedin.com/company/software-for-chemistry-&-materials
>
>
>
> _______________________________________________
> ADFlist mailing list
> ADFlist at scm.com
> https://lists.scm.com/mailman/listinfo/adflist
>
>
> Dr. T. P. M. (Fedor) Goumans
> Business Developer
> Software for Chemistry & Materials
> Vrije Universiteit, FEW, Theoretical Chemistry
> De Boelelaan 1083
> 1081 HV Amsterdam, The Netherlands
> T +31 20 598 7625
> https://www.scm.com
> https://twitter.com/SCM_Amsterdam
> https://www.linkedin.com/company/software-for-chemistry-&-materials
>
>
>
>
> _______________________________________________
> ADFlist mailing list
> ADFlist at scm.com
> https://lists.scm.com/mailman/listinfo/adflist
>
>


-- 
Dr. Nuha Wazzan
Associate Professor of Physical Chemistry

School of Chemistry
King Abdulaziz University
P.O Box 42805
Jeddah 21551
Saudi Arabia

e-mail: nwazzan at kau.edu.sa

-- 
Disclaimer: The information contained in this message is intended for the 
addressee only and may contain classified information. If you are not the 
addressee, please delete this message and notify the sender; you should not 
copy or distribute this message or disclose its contents to anyone. Any 
views or opinions expressed in this message are those of the individual(s) 
and not necessarily of the university. No reliance may be placed on this 
message without written confirmation from an authorized representative of 
its contents. No guarantee is implied that this message or any attachment 
is virus free or has not been intercepted and amended. 

إخلاء مسؤليه:  ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم، وربما 
تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة واشعار 
المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين. ويجدر 
بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية وليست 
بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم تحصل على 
موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه الرسالة أو 
مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.scm.com/pipermail/adflist/attachments/20171017/ee381485/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 169030 bytes
Desc: not available
URL: <https://lists.scm.com/pipermail/adflist/attachments/20171017/ee381485/attachment-0001.png>


More information about the ADFlist mailing list