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Questions related from Barış Kurt
I prepared a 23-page article on parameterization. I submitted the article to a journal known as "good" in its field. After keeping my article for 4 months, the journal suggested a revision....
29 June 2023 7,341 6 View
Hello, I want to dock a molecule including boron atom. Autodock is very slow so I want to use vina.exe instead of it. I change atom_constans variables in the source code. But after that I couldn't...
29 November 2019 9,162 2 View
I installed AmberTools18 and I installed MPI libraries as well. Everthing is working but when I want to run sander parallel like this: mpirun -np 32 sander.MPI -O -i min.in -o min.out -p...
18 July 2019 10,248 7 View
Hi all, I am trying to generate a force field for a new molecule. I obtained bond foce constants but I don't know how to obtain angular force constants. Could you provide me a solution? Thank you.
16 March 2018 9,388 2 View
Hi, I am trying to make a *.dat file manually and I calculated force constant with gaussian. In gaussian force const. units are:mdyne/A but in *.dat files it is: kcal/molA^2 after that I found...
14 March 2018 9,317 2 View
Hi, other molecules is basic but B elemement is not in gaff.dat and I can't use ante-chamber. So How can I generate topology for an element not including in gaff??
10 March 2018 9,786 3 View
Hi, My Ph.D. thesis is : To obtain a new amber forcefield by calculating (I will use GAUSSIAN09 for QM) the necessary parameters for bonds such as X-C X-C-H X-H for X element, not included in Gaff...
08 March 2018 3,367 3 View
Hi, I calculated PED data with VEDA but I don't know which vibrations are asymmetric or symetric. How could I decide it? For example: s 1 1.00 STRE 13 18 CH 1.086848 f3207...
02 March 2017 7,886 3 View
