7 Questions 25 Answers 0 Followers
Questions related from Barış Kurt
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...
07 July 2019 4,641 6 View
I am trying to develop parameters for AMBER FF and calculate Lennard-Jones parameters for Fe+3 ion. I really did a deep search and I found that it is the best way to use TDDFT for this with a high...
01 January 2019 3,190 2 View
I am trying to let's say BH3 imroper force constantsfor Amber force field. Normally scan dihedral angels and obtain values I want. But As far as I know, Gaussian is not capable of using...
01 January 2019 5,883 4 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...
03 March 2018 4,812 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??
03 March 2018 4,967 3 View
Hi, in gaussian FTIR log file, all force constant units are mdyne/A. It doesn't matter for gaussian the vibration belongs to bond or angle it uses the same unit. But Amber gaff file uses...
03 March 2018 1,221 3 View
Hi, I calculated PED datas 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...
03 March 2017 7,927 4 View
