Error! Invalid Amino Acid HIE

[Russell B. Davidson]

I'm incorporating the SPECS analysis code into a open-source pipeline to evaluate folded protein structures obtained from molecular dynamics simulations. I'm using the AmberTools20 tleap and sander packages, which specifies various residue names for histidine associated with its various protonation states. SPECS doesn't like the resnames HIE and HIP. Can these be added to the list of protein residues?

[Russell B. Davidson]

The HIE and HIP resnames are the most common nonstandard resnames to be used in MD simulations using AMBER parameters. The ff14SB parameter has numerous other nonstandard residue names: ASH, CYM, CYX, GLH, HYP, and LYN.

Maybe adding an exhaustive list of resnames used in MD parameter sets is nontrivial... But adding some of the common resnames would be hugely beneficial for those trying to use SPECS for evaluation of MD simulations.

[Russell B. Davidson]

Have written code to pre-process structures before reading them into SPECs.