From 73f863a6ab25d92420c095180c76a0876c985865 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Fri, 8 Sep 2017 09:09:09 +0200
Subject: [PATCH] Implicit: small changes
---
src/colvar/Implicit.cpp | 34 ++++++++++++++++++++++++++--------
1 file changed, 26 insertions(+), 8 deletions(-)
diff --git a/src/colvar/Implicit.cpp b/src/colvar/Implicit.cpp
index ab4e21f07..54c5a548f 100644
--- a/src/colvar/Implicit.cpp
+++ b/src/colvar/Implicit.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017 The plumed team
+ Copyright (c) 2016,2017 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -42,10 +42,9 @@ namespace colvar {
//+PLUMEDOC COLVAR IMPLICIT
/*
+Calculates EEF1 solvation free energy for a group of atoms.
-Calculate EEF1-SB solvation free energy for a group of atoms.
-
-EEF1-SB is a solvent-accessible surface area based model, where the free energy of solvation is computed using a pairwise interaction term for non-hydrogen atoms:
+EEF1 is a solvent-accessible surface area based model, where the free energy of solvation is computed using a pairwise interaction term for non-hydrogen atoms:
\f[
\Delta G^\mathrm{solv}_i = \Delta G^\mathrm{ref}_i - \sum_{j \neq i} f_i(r_{ij}) V_j
\f]
@@ -133,8 +132,7 @@ Implicit::Implicit(const ActionOptions&ao):
checkRead();
- log << " Bibliography " << plumed.cite("Bottaro S, Lindorff-Larsen K, Best R, J. Chem. Theory Comput. 9, 5641 (2013)")
- << plumed.cite("Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)"); log << "\n";
+ log << " Bibliography " << plumed.cite("Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)"); log << "\n";
nl.resize(size);
@@ -287,6 +285,7 @@ void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<dou
valuemap = setupValueMap();
typemap = setupTypeMap();
vector<SetupMolInfo*> moldat = plumed.getActionSet().select<SetupMolInfo*>();
+ bool cter=false;
if (moldat.size() == 1) {
log << " MOLINFO DATA found, using proper atom names\n";
for(unsigned i=0; i<atoms.size(); ++i) {
@@ -297,7 +296,7 @@ void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<dou
string Atype = typemap[Rname][Aname];
// Check for terminal COOH or COO- (different atomtypes & parameters!)
- if (moldat[0]->getAtomName(atoms[i]) == "OT1") {
+ if (moldat[0]->getAtomName(atoms[i]) == "OT1" || moldat[0]->getAtomName(atoms[i]) == "OXT") {
// We create a temporary AtomNumber object to access future atoms
unsigned ai = atoms[i].index();
AtomNumber tmp_an;
@@ -309,8 +308,9 @@ void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<dou
// COO-
Atype = "OC";
}
+ cter = true;
}
- if (moldat[0]->getAtomName(atoms[i]) == "OT2") {
+ if (moldat[0]->getAtomName(atoms[i]) == "OT2" || (cter == true && moldat[0]->getAtomName(atoms[i]) == "O")) {
unsigned ai = atoms[i].index();
AtomNumber tmp_an;
tmp_an.setIndex(ai + 1);
@@ -372,6 +372,15 @@ void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<dou
map<string, map<string, string> > Implicit::setupTypeMap() {
map<string, map<string, string> > typemap;
typemap = {
+ { "ACE", {
+ {"CH3", "CT3"},
+ {"HH31","HA3"},
+ {"HH32","HA3"},
+ {"HH33","HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
{ "ALA", {
{"N", "NH1"},
{"HN", "H" },
@@ -711,6 +720,15 @@ map<string, map<string, string> > Implicit::setupTypeMap() {
{"O", "O" }
}
},
+ { "NMA", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CH3", "CT3"},
+ {"HH31","HA3"},
+ {"HH32","HA3"},
+ {"HH33","HA3"},
+ }
+ },
{ "PHE", {
{"N", "NH1"},
{"HN", "H" },
--
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