Cheminformatics and Computational Chemistry

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15 Are there any free workstation software for QSAR?
By Arvind Kumar · Sri Sathya Sai Institute of Higher Learning

Flavio Ballante · Sapienza University of Rome

Dears, the 3-D QSAutogrid/R procedure, together with tutorials, will begin to be available from October; from that date you will find them in www.3d-q... [more]

Dears, the 3-D QSAutogrid/R procedure, together with tutorials, will begin to be available from October; from that date you will find them in www.3d-qsar.com. With best regards, FB

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6 What are criteria for good definitions of chemical space and descriptors?
By Anatole von Lilienfeld · Argonne National Laboratory

Andrea Mauri · Università degli Studi di Milano-Bicocca

As I already wrote you the are few rules, recognized by the whole community that uses molecular descriptors, that a molecular descriptor should follow... [more]

As I already wrote you the are few rules, recognized by the whole community that uses molecular descriptors, that a molecular descriptor should follow. These rules are those reported in the tutorial I suggested.Prof. Milan Randic, Prof.Todeschini and Consonni are three of the most important researchers in the field of molecular descriptors. Randic index is one of the most used and famous molecualr descriptor. Besides these rules a descriptor is good if it is good to model something.

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17 How to obtain a transition state (TS) for a SN2 reaction involving phosphorus as the center of nucleophilic attack?
By Lucas Esteves · Universidade Federal de Juiz de Fora

Lucas Esteves · Universidade Federal de Juiz de Fora

First and foremost I would like to thanks all the replies. This discussion has been extremely helpful to me. I found the transition state using two ... [more]

First and foremost I would like to thanks all the replies. This discussion has been extremely helpful to me. I found the transition state using two functional: mPW1PW91 and mPW1K as suggested by Ramon Crehuet, John Wilkie and Daniel Coimbra who suggested the article "A qualitative failure of B3LYP for textbook organic reactions". This kind of reaction should pass through a transistion state, because only phosphate monoester may pass through pentacoordinated intermediates. George Fitzgerald, I will try this functional also. Jorge Ignacio Martinez-Araya, I didn't tried QST2 or QST3 options because I had no idea how the intermediates looks. Olga Dmytrenko the next step is to try to obtain the transition state using continuum models. But thanks for your suggestion. So ... Thank you all for the help, it was a great contribution, Sorry for my english. My best regards

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2 Open Source software for screening of Chemical compounds based on Pharmacophore
By Shameer Pillarisetti ·

Shameer Pillarisetti ·

Thank Mikko Vainio for your reply

Thank Mikko Vainio for your reply

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Answer added to:
5 Quantum espresso
By Nasser Zamand · Ferdowsi University Of Mashhad

Alexander Kulesza · CreativeQuantum GmbH

@Anatole: You are completely right, i would not deny that running a DFT calculation yields identical results in the limit of totally converged calcula... [more]

@Anatole: You are completely right, i would not deny that running a DFT calculation yields identical results in the limit of totally converged calculation parameters. Nevertheless, the approaches taken by both codes is completely different. From practical points of view, I personally would not use QE for Excited States of gasphase Molecules, Gas-Phase Reactions, Hybrid-Functionals, Photochemistry, Open-Shell Metal-complexes, while i would not think about calculating something like transport properties in metal-semiconductor heterojunctions with Gaussian or Turbomole as a first attempt. I hope that, taking this into account, my statement is more clear .

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3 What is the best method to calculate biological cofactors (FeMo) using DFT?
By Alexander Ivanov · Utah State University

Olga Dmytrenko · University of Delaware

Agree with all said above. We used B3LYP and CASSCF for the “Somersault” mechanism for the P-450 hydroxylation of hydrocarbons: http://pubs.acs.or... [more]

Agree with all said above. We used B3LYP and CASSCF for the “Somersault” mechanism for the P-450 hydroxylation of hydrocarbons: http://pubs.acs.org/doi/abs/10.1021/ja052111%2B

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4 How to design a drug in manual for a disease?
By Shameer Pillarisetti ·

Lesitha J · Vellore Institute of Technology

Identify the pharmacophore onto which you can substitute these groups. This can be done by identifying the common backbone of the active drugs that ar... [more]

Identify the pharmacophore onto which you can substitute these groups. This can be done by identifying the common backbone of the active drugs that are in use. You can probably use the common feature pharmacophore of Accelrys software.

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9 How does VMD program compile from source code with NVIDIA GeForce (GPU)?
By Hiroaki Tokiwa · Rikkyo University

Daniel Vasquez

NVIDIA does not support Linux. In Linus' own words: http://www.youtube.com/watch?v=MShbP3OpASA#t=2993s

NVIDIA does not support Linux. In Linus' own words: http://www.youtube.com/watch?v=MShbP3OpASA#t=2993s

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Question:
Open Does anyone have detailed tutorial on OPEN3DQSAR software ?
The tutorial available on website is not so detailed. I am completely new to command line programs. So does anyone have detailed tutorial?

The tutorial available on website is not so detailed. I am completely new to command line programs. So does anyone have detailed tutorial?

By Arvind Kumar · Sri Sathya Sai Institute of Higher Learning

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3 I am using Dalton2011 electronic structure progam, for the calculation of electronic excitation energies for a series of molecules.
By Alamgir Khan · Universidade Estadual de Campinas

Alamgir Khan · Universidade Estadual de Campinas

Thank you very much Tatiana....

Thank you very much Tatiana....

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3 Statistical Approaches in Cheminformatics
By Pritish Dash · Institute of Bioinformatics and Applied Biotechnology

Ara Kooser · University of New Mexico

Also see Charting, Navigating, and Populating Natural Product Chemical Space for Drug Discovery http://pubs.acs.org/doi/abs/10.1021/jm300288g

Also see Charting, Navigating, and Populating Natural Product Chemical Space for Drug Discovery http://pubs.acs.org/doi/abs/10.1021/jm300288g

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Answer added to:
2 NWChem benchmark performance on Amazon EC2?
By Jonathan Reyles · San Jose State University

Patrick Nichols · Pacific Northwest National Laboratory

I agree totally with Wibke. I worked on NWChem as a post-doc and I can say from my own work that the performance is _very_ dependent on what interconn... [more]

I agree totally with Wibke. I worked on NWChem as a post-doc and I can say from my own work that the performance is _very_ dependent on what interconnect you use. I would expect 3-10 times slower performance when compared to infiniband depending on the number of nodes you are using. One reason is that Global Arrays/ARMCI is not optimized for 10G so you are using the old sockets interface. If you still want to go ahead and use the cloud you should probably contact the NWChem's user list for more in depth advice ( https://www.nwchem-sw.org )... Hope that helps.

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Answer added to:
1 SAPT installation -reg
By Venkatesan Srinivasadesikan · National Chung Cheng University

Tatiana Korona · University of Warsaw

I understand that you followed the installation instructions given on the SAPT web page and did not succeed? I suggest to ask Konrad Patkowski, [email... [more]

I understand that you followed the installation instructions given on the SAPT web page and did not succeed? I suggest to ask Konrad Patkowski, [email address deleted], who made this interface.

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Answer added to:
4 Multiple sequence alignment
By Karthik Kandasamy · Tamil Nadu Agricultural University

Insung Ahn · Korea University of Science and Technology

If your final goal is to build a phylogenetic tree, you must reduce the amount of taxa numbers because although you succeed to calculate tree, it will... [more]

If your final goal is to build a phylogenetic tree, you must reduce the amount of taxa numbers because although you succeed to calculate tree, it will be difficult to draw a tree. About the multiple sequence alignment, you must use Linux-based clustalw or other programs instead of Windows-based beause of the memory probelm. And if possible, use the queuing system to perform your calculating job in batch condition. Some times, multiple sequence alignment takes several days.

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Question:
Open What is the structure of CeNiO3?
Perovskite structure

Perovskite structure

By Gopi Mohan · Amrita Vishwa Vidyapeetham

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4 Software for predicting synthetic accessibility
By Heru Pratomo · University of Indonesia

Bojja Rajeshwar Rao · Kakatiya Thermal Power Project, Chelpur-506 170, India

Dear Sir, Frontier Orbital Theory will tell us the possibility of synthesis of organic molecules, Please refer application of Frontier Orbital Theory ... [more]

Dear Sir, Frontier Orbital Theory will tell us the possibility of synthesis of organic molecules, Please refer application of Frontier Orbital Theory to the Organic Molecule synthesis in the google.com You will get lot of literature for the prediction of synthesis of a new molecule from respective reactants theoretically,.

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19 Good software for DNA & RNA 3D structure prediction?
By Muhammad Sulaman Nawaz · COMSATS Institute of Information Technology

Christian Schudoma · Max-Planck-Institut für molekulare Pflanzenphysiologie

@Steven Combs: The Rosetta method for RNA is called FARNA (with FARFAR extension) and I listed it in one of the earlier answers, even mentioning that ... [more]

@Steven Combs: The Rosetta method for RNA is called FARNA (with FARFAR extension) and I listed it in one of the earlier answers, even mentioning that it's "basically Rosetta for RNA". Checking the whole thread and searching for keywords sometimes helps to avoid being surprised ;D

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13 Metal co-factor and ligand interactions during docking studies
By Pawan Gupta · National Institute of Pharmaceutical Education and Research

Mukesh Yadav · Softvision College, Indore, M.P. INDIA- 452010

You can use GOLD. it will help you to include metal ion or any hetero atom along with variety of options in terms of interactions

You can use GOLD. it will help you to include metal ion or any hetero atom along with variety of options in terms of interactions

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8 How to calculate delocalization energy using Gaussian 09?
By Soumen Ghosh · Indian Institute of Technology Bombay

Mohammad Alam · Aligarh Muslim University

let me know all Link 0 Commands, Route section (# lines) and keywords that you have used.

let me know all Link 0 Commands, Route section (# lines) and keywords that you have used.

Following
Question:
Open Considering fuel cell ammonia is good for proton transfer, has anyone had experience with, or are there any references to use of ammonia in polymer electrolyte membranes?
Specifically, in polymer electrolyte membranes such as PBI (poly-benzimidazole) with phosphoric acids.

Specifically, in polymer electrolyte membranes such as PBI (poly-benzimidazole) with phosphoric acids.

By Manoj Mane · National Chemical Laboratory

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3 Is it possible to use Heterogeneous reaction rate equation from different sources in one calculation?
By Kim Wonseok · Korea University of Science and Technology

Kim Wonseok · Korea University of Science and Technology

Thanks for reply

Thanks for reply

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Answer added to:
7 How to calculate optimized structure in nth excited states using Gaussian?
By Mohammad Alam · Aligarh Muslim University

Alexander Kulesza · CreativeQuantum GmbH

Hi... look for the gaussian documentation of obtaining Franck-Condon factors. From that you can construct vibrationally resolved optical spectra. Its ... [more]

Hi... look for the gaussian documentation of obtaining Franck-Condon factors. From that you can construct vibrationally resolved optical spectra. Its mentioned in the "Freq" keywords section: "ELECTRONIC EXCITATION ANALYSIS OPTIONS". There is, to my knowledge, no easy way to obtain operator expectation values bewtween different electronic TDDFT states. But a detailed study of the IOps may reveal some prospects.

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Answer added to:
4 Label of electronic states/configurations
By Mohammad Alam · Aligarh Muslim University

Mohammad Alam · Aligarh Muslim University

Thank-you very much

Thank-you very much

Following
Question:
Open Vibronic structure using Gaussian 09
How to calculate vibrationally resolved electronic structure using Gaussian 09?

How to calculate vibrationally resolved electronic structure using Gaussian 09?

By Mohammad Alam · Aligarh Muslim University

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Answer added to:
3 How can I calculate photoabsorption spectra in Vacuum UV region using Gaussian 09?
By Mohammad Alam · Aligarh Muslim University

Alexander Kulesza · CreativeQuantum GmbH

there is only a practical limit in RAM and cpu time for the calculation. The bigger the number of excited states you want to determine, the bigger the... [more]

there is only a practical limit in RAM and cpu time for the calculation. The bigger the number of excited states you want to determine, the bigger the quasi-eigenvalue tddft problem. For a 50 atom molecule around 100 states are still feasible on a small computercluster. Rydberg states are a problem in tddft. They are in general not well described. If dealing with Rydberg states, a basis with diffuse functions is mandatory. Nevertheless, accurate transition energies are not to be expected (i do not have experience with Rydberg states and long-range corrected functionals, they may perform better).

Following
Question:
Open Reactive hybrid orbital (RHO) method
Does any one know about RHO method, how to do calculations in Gaussian 09/03?

Does any one know about RHO method, how to do calculations in Gaussian 09/03?

By Yernaidu Reddi · Indian Institute of Technology Bombay

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13 Where can I find force field parameters for pirazinamide?
By Carlos Bueno · Universidad Peruana Cayetano Heredia

Visvaldas Kairys · Vilnius University

Some parameters sets such as MMFF94 are available in openbabel http://openbabel.org, with Avogadro http://avogadro.openmolecules.net/ as a GUI.

Some parameters sets such as MMFF94 are available in openbabel http://openbabel.org, with Avogadro http://avogadro.openmolecules.net/ as a GUI.

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5 Interesting read for budding molecular modelers!
By Yogesh Wagh · University of Pune

Nousheen Mushtaq · University of Karachi

Very good! helping material for many students

Very good! helping material for many students

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About Cheminformatics and Computational Chemistry

Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids.

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