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graeter-group / kimmdy

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
https://graeter-group.github.io/kimmdy/
GNU General Public License v3.0
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Amino acid histidine not correctly handled by KIMMDY #384

Open emerbitz opened 8 months ago

emerbitz commented 8 months ago

Histidine is denoted as HIS in the .top-file, when the .top-file is generated from a amino acid sequence via pymol fab and pdb2gmx. However, the amber force field encompasses not HIS but HIP, HID, and HIE. Thus, HIS is not found in the force field. However, when a bond is formed with Topology.bind_bond, it needs the amino acid information. Maybe also for change_partial_charges? Possible solutions: Add HIS to forcefield or change HIS in .top-file.

Should there be a solution within kimmdy to convert HIS and similar aminoacids automatically to the corresponding aminoacids.rtp entry?

jmbuhr commented 8 months ago

hm, pdb2gmx should choose the right histidine type based on a crude estimation of its protonation state. Was pdb2gmx run with the same ff as kimmdy afterwards?

ehhartmann commented 8 months ago

I think pdb2gmx sees HIS in the pdb and keeps the protonation state but also keeps the name HIS or you dynamically select the protonation state per his residue and it calls it HISD, HISE, HISP but never like the original ff entries HID, HIE, HIP. The collagen fibril also has HIS.

jmbuhr commented 8 months ago

https://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html

... for His the proton can be either on ND1, on NE2 or on both. By default these selections are done automatically. For His, this is based on an optimal hydrogen bonding conformation.

ehhartmann commented 8 months ago

Ah okay, so they guess it. Still, they don't change the residue name based on the protonation state and that's the problem. edit: or they change it but not to the residuetypes.dat entry.