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Questions related to Computational Chemistry
I have a set of PDB structures of proteins and I want to calculate cavity volume of each protein. Is there any trusted software or online server for this purpose? Thanks in advance.
18 August 2017 6,278 1 View
I have one host molecule and one guest molecule. The host molecule contains Zn+2 interacting with four nitrogens that belong to the same host. Initially, negatively charged oxygens each from two...
21 July 2017 7,771 5 View
I am trying to do a geometry optimization of my structure with some constraints however when I check the .out file during the run it does not proceed to further stages. What I mean by that is that...
19 July 2017 1,253 10 View
I am trying to model the active sites of several MOF's using Gaussian 09 Unix package. One such MOF I have to model is MIL-100 and I am constantly finding difficulties in obtaining a converged...
05 July 2017 2,757 3 View
I have a host-guest solution in an aprotic solvent medium. I suspect that there is a probability of existence of anion- π interaction during host-guest recognition process. What is the simple and...
23 May 2017 7,733 8 View
The PBC calculation is on a polymer chain in which non-covalent interactions is important. I'm attempting to calculate the crystal geometry, lattice parameters, and overall crystal packing. I'm...
03 May 2017 7,034 2 View
Which are the considerations needed, especially regarding symmetry, when I simulate a supercell formed by two different types of unit cells? For example, what would happen if it is formed by four...
24 April 2017 7,583 5 View
I am trying to find the reaction pathway of an enzymatic reaction using the QST2 keyword in Gaussian. I am modeling the active site with the two amino acid residues identified to be taking part...
27 February 2017 6,213 3 View
Dear colleagues, I'm beginner in C++ programming, I've coded a c++ program to solvate (hydrate) a structure (carbon nanotube for instance). Would you please check it out and give me your comments...
04 February 2017 7,405 9 View
In the hypothetical case of a system that may require crossing between manifolds of different multiplicities: Two PESs are created for a heavy atom abstracting a hydrogen atom. One is the triplet...
26 January 2017 7,415 7 View
I began running IRC calculations from the optimized TS. Before starting irc I did frequency calculation which confirm that my Ts is stationary point and the first frequency is negative. But IRC...
30 November 2016 9,339 6 View
how can i split the zinc SDF file?pls explain step by step procedure
16 April 2016 5,893 1 View
I want to know some free software for protein computational chemistry with: 1. very good GUI facility 2. ease of use with good interactive facilities Please provide your valuable suggestions and...
04 April 2016 5,574 3 View
Dear all Sometimes in opt+freq calculation, the structure gives 5-10 cm-1 of imaginary frequency regardless of no. of the minimum search operation. So in this case can we assume 5-10 cm-1 of...
03 April 2016 340 8 View
We arrived at this when using the driving approach, after finding two close breaks in energy profile. We started optimizations to TS from structures closest to each of these two breaks and arrived...
01 April 2016 6,748 3 View
Hello, I'm new to GAMESS Interface (in Chem3D). Each function/prediction/calculation gives me an error: An error has occurred during the GAMESS calculation. Output file is not created. Can anyone...
31 March 2016 1,330 6 View
Dear researchers, When, for example, LanL2DZ basis set is used for a heavy metal such as Ag (Silver), Gaussian divides its electrons to effective core and valence electrons. The question is that...
31 March 2016 5,764 5 View
Dear Researchers, While both of 3-21G and LanL2DZ basis sets work on In (Indium), which one is more appropriate to be used when InCl3 is considered as a Lewis acid catalyst? Many thanks, Saeed
31 March 2016 7,055 7 View
I am doing singlet energy level calculations of a molecule which is having 130 atoms. the optimization of the compound done by using B3LYP/6-31G(d,p), in 64bits-windows. the optimization done...
30 March 2016 1,161 7 View
Is there any general rule for determine which element will make V.B and which will make C.B. For example if I want to know in TiO2 which element will make V.B and which will make C.B.
25 March 2016 327 2 View
Can you propose a model theory and basis set to be used in the computational studies of cyclic carbenes (cycloprpene carbene). Is it okay to apply to for both singlet and triplet states? Thanks...
25 March 2016 5,203 2 View
computational chemistry, DFT, material modeling
24 March 2016 9,726 2 View
I am modeling a Nafion 117 proton exchange membrane and I want to determine the concentration of hydrogen ions inside this membrane when it is fully hydrated.
22 March 2016 6,859 1 View
Hi, i am a beginner in AIMD, i want to simulate a geometry optimization of a protonated dimer. My jobs did not run anyway. these are my inputs. Tanks.
08 March 2016 7,089 2 View