VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jun 15 2018 - 04:51:49 CDT

Hi Nick,

Unless you need a specific chirality or geometry, IC tables aren't actually required in a topology file. For the protein part of mCherry, standard topology files only have IC tables to specify the handedness of the amino acid. For the flurophore you are adding in (I assume there is a flurophore?), the heavy atoms alone are enough to specify the position of stray hydrogens, since only sites with 1 hydrogen can be chiral. So basically I would prepare a topology file without an IC table, and then let psfgen guess where the hydrogens need to go. It won't be perfect, but it should be close enough.

-Josh

On 2018-06-14 13:09:15-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Hello everyone, I am making a topology file for the chromophore in the mCherry protein and I I need to add hydrogens to the molecule in order to get IC values in a table. I have tried using molefacture, however every time I add the hydrogens to the molecule and write it to a pdb, several carbon atoms end up missing from the file. I have also tried getting the IC values from the xbgf file generated from the molefacture, but it doesn't generate anything I can really use. Is there an easier way to do this that I am not aware of? 

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Nicholas J. Palmer