From 409005942429428162837ae66ceacb0de69181f3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 1 Nov 2022 11:48:34 +0100
Subject: [PATCH] Ensure correct elements for terminal oxygens when using AMBER
forcefield
---
modules/mol/mm/src/topology_creator.cc | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index dede191f8..00ba0738d 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -164,6 +164,21 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(hc){
hc->ApplyOnBuildingBlock(block);
hc->ApplyOnResidue(*i,ed);
+ // hack for AMBER forcefield
+ // GROMACS hijacks the hydrogen constructor to construct terminal oxygens
+ // in the case of the AMBER forcefield, their elements are thus set to H.
+ // Forcefields in general don't care about elements, they just care for
+ // atom types and their respective masses. There is no easy way to tell
+ // the hydrogen constructor that the element is not H. I just hardcode the
+ // AMBER case here. Please forgive me...
+ ost::mol::AtomHandle at = i->FindAtom("OC1");
+ if(at.IsValid()) {
+ at.SetElement("O");
+ }
+ at = i->FindAtom("OC2");
+ if(at.IsValid()) {
+ at.SetElement("O");
+ }
}
//check for n terminus
if(i->HasProp("n_ter")){
--
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