Hello,
I was passed an older simulation that was originally done in 2016. I no longer have any of the original input files and only have vmd modified DRUDE pdb files, its corresponding .xplor file and the 2013 charm topologies.
I am wanting to mostly keep this system intact as charm-gui has gotten rid of the homogenous membrane builder and this exact system would be difficult to replicate, but I need to add in additional ions and then again regenerate a DRUDE .xplor file for these additional charges. I have tried adding this pdb file into Charmm-Gui and it appears unable to read it, even after I added in the ter and chain IDs that VMD generated pdb files typically need.
I found that psfgen was modified to be able to output Drude .psf files, however I cannot use the same 2013 charm generated topologies for this, and would need to use the new 2020 charm topologies. This in itself wouldn't be a big deal, however vmd does not seem to recognize SWM4 as a water ion, and I cannot find any way listed on the internet to add in ions, and then generate a DRUDE .psf file from a previous DRUDE simulation. Does anyone have any ideas?
Thanks!
Dear Hannah Burton
These links might be useful, have a look:
1. https://www.ks.uiuc.edu/Research/namd/2.9/ug/node25.html
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516320/
3. http://www.ks.uiuc.edu/Training/Tutorials/qwikmd/qwikmd-tutorial.pdf
4. https://pubs.acs.org/doi/10.1021/jp503469s
5. https://academic.oup.com/nar/article/48/2/561/5661083
Kind Regards
Qamar Ul Islam
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