VMD-L Mailing List

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Wed Jun 20 2018 - 12:42:00 CDT

Thanks for the reply,
I took your advice and stopped trying to make an IC table, instead I
manually added the hydrogens to the pdb file from the one I generated
before. The topology file seems to work for the most part with this.

On Fri, Jun 15, 2018 at 5:51 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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?
> --
> Nicholas J. Palmer
>
> 

-- 
Nicholas J. Palmer