VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Aug 09 2022 - 08:09:41 CDT

Hi,

I am using QwikMD to prepare simulation files and my PDB file includes a sialic acid, so I get an error that there is unknown topology for the three residues of the sialic acid. I clicked Add Topo+Param, and then clicked the + sign and selected the top_all36_carb.rtf file. This automatically loaded various residue names in the Topology & Parameters Selection window, several of which I had to rename the CHARMM name for as they exceeded four letters/numbers. I assume these are the various atoms that comprise the three "residues" of the sialic acid. I then selected Apply and got a warning that these topologies and parameters would be added to the QwikMD library, to which I selected Okay. A warning message then appeared to reset QwikMD to ensure that the proper topologies load. I clicked the Reset button and then reloaded my PDB file.

However, in the Structure Manipulation Window I still get an error that the topologies and parameters are missing for all three "residues" of the sialic acid. If I click Add Topo+Param, the various residues/atoms for which I renamed the CHARMM names and added the topologies are already loaded. Therefore, I am not sure why I continue to get an error that there is missing topology and parameters for the sialic acid.

Is it something to do with the ResName in the main Structure Manipulation window? For example, the three residues of the sialic acid are named BGC, GAL, and SIA. Do these need to match a RESI code from the top_all36_carb.rtf file?

If yes, how do I change the ResName? If I click Rename in the structure manipulation window and try to rename it, the only options I have are to select from things like ATP, NADH, etc. and not type something. Additionally, if there is no matching residue in the .rtf file, do I need to create a custom topology/parameter file?

I have tried reading the manual for QwikMD but I cannot find any information regarding why I continue getting a missing topology error. Are there any steps I am missing for adding the topology/parameters for non-standard molecules in QwikMD?

Thank you for any help, it is greatly appreciated.