The VMD manual at www.ks.uiuc.edu/Research/vmd/plugins/saltbr/ said for the output files, this distance is slightly different than the criteria used to identify salt bridges. I got a salt bridge dat file with all the distances more than 3.2 (min is 4.4). So it is difficult to know the "slightly different".
Hi Bro, we noticed that VMD salt bridge plugin can't recognize any other polarized or charged atoms than protein's. How to calculate salt bridges between polar lipid and residue atoms?
The VMD manual at www.ks.uiuc.edu/Research/vmd/plugins/saltbr/ said for the output files, this distance is slightly different than the criteria used to identify salt bridges. I got a salt bridge dat file with all the distances more than 3.2 (min is 4.4). So it is difficult to know the "slightly different".
Thanks very usefull
thx
Love your videos! Can you show us how to plot this? Thank you so much!
python!
Hi Bro, we noticed that VMD salt bridge plugin can't recognize any other polarized or charged atoms than protein's. How to calculate salt bridges between polar lipid and residue atoms?
Should we really use psf file? Is it also okay to use pdb instead it?
can I visualize these calculated salt bridges?