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SAXS onebead case
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- new CYX
- fixes for non contigues numbering in template pdb files
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@carlocamilloni
carlocamilloni committed May 23, 2024
1 parent 9b42025 commit d4f7b55
Showing 1 changed file with 148 additions and 36 deletions.
184 changes: 148 additions & 36 deletions src/isdb/SAXS.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,8 @@ Two additional bead types are available for DNA and RNA besides phosphate group,
"5", e.g., DC5 or C5 for cytosine in DNA and RNA, respectively);
- 3'-end pentose sugar capped with an hydroxyl moiety at C3' (the residue name in the PDB must be followed by
"3", e.g., DC3 or C3 for cytosine in DNA and RNA, respectively).
An additional bead type is available for proteins:
-Cysteine residue involved in disulfide bridge (the residue in the PDB must be named CYX).
Experimental reference intensities can be added using the EXPINT keywords. All these values must be normalised
to the SAXS intensity at q = 0. To facilitate this operation, the SCALE_EXPINT keyword can be used to provide
Expand Down Expand Up @@ -181,6 +183,8 @@ Two additional bead types are available for DNA and RNA besides phosphate group,
e.g., DC5 or C5 for cytosine in DNA and RNA, respectively);
- 3'-end pentose sugar capped with an hydroxyl moiety at C3' (the residue name in the PDB must be followed by "3",
e.g., DC3 or C3 for cytosine in DNA and RNA, respectively).
An additional bead type is available for proteins:
-Cysteine residue involved in disulfide bridge (the residue in the PDB must be named CYX).
PLEASE NOTE: at the moment, we DO NOT explicitly take into account deuterated residues in the ATOMISTIC
representation, but we correct the solvent contribution via the DEUTER_CONC keyword.
Expand Down Expand Up @@ -251,11 +255,40 @@ class SAXS :
DG_3TE, DG_5TE, DG_TE3, DG_TE5, DT_BB1, DT_BB2, DT_BB3, DT_SC1, DT_SC2, DT_SC3, DT_3TE,
DT_5TE, DT_TE3, DT_TE5, NMARTINI
};
enum { TRP, TYR, PHE, HIS, HIP, ARG, LYS, CYS, ASP, GLU, ILE, LEU, MET, ASN, PRO, GLN, SER, THR, VAL, ALA, GLY,
BASE_A, BASE_C, BASE_T, BASE_G, BASE_U,
BB_DNA, BB_DNA_5, BB_DNA_3,
BB_RNA, BB_RNA_5, BB_RNA_3,
enum { TRP,
TYR,
PHE,
HIS,
HIP,
ARG,
LYS,
CYS,
CYX,
ASP,
GLU,
ILE,
LEU,
MET,
ASN,
PRO,
GLN,
SER,
THR,
VAL,
ALA,
GLY,
BB_PO2,
BB_DNA,
BB_DNA_5,
BB_DNA_3,
BB_RNA,
BB_RNA_5,
BB_RNA_3,
BASE_A,
BASE_C,
BASE_T,
BASE_G,
BASE_U,
NONEBEAD
};
struct SplineCoeffs {
Expand Down Expand Up @@ -709,7 +742,7 @@ SAXS::SAXS(const ActionOptions&ao):
std::vector<std::vector<long double> > parameter_vac(NONEBEAD);
std::vector<std::vector<long double> > parameter_mix(NONEBEAD);
std::vector<std::vector<long double> > parameter_solv(NONEBEAD);
getOnebeadparam(pdb, atoms, parameter_vac, parameter_mix, parameter_solv,residue_atom);
getOnebeadparam(pdb, atoms, parameter_vac, parameter_mix, parameter_solv, residue_atom);
for(unsigned i=0; i<NONEBEAD; ++i) {
for(unsigned k=0; k<numq; ++k) {
for(unsigned j=0; j<parameter_vac[i].size(); ++j) {
Expand Down Expand Up @@ -787,6 +820,7 @@ SAXS::SAXS(const ActionOptions&ao):
Iq0 *= Iq0;
}


std::vector<double> expint;
expint.resize( numq );
ntarget=0;
Expand Down Expand Up @@ -948,13 +982,16 @@ SAXS::SAXS(const ActionOptions&ao):
}

log<<" Bibliography ";
if(onebead) {
log<<plumed.cite("Ballabio, Paissoni, Bollati, de Rosa, Capelli, Camilloni, J. Chem. Theory Comput., 19, 22, 8401-8413 (2023)");
}
if(martini) {
log<<plumed.cite("Niebling, Björling, Westenhoff, J Appl Crystallogr 47, 1190–1198 (2014)");
log<<plumed.cite("Paissoni, Jussupow, Camilloni, J Appl Crystallogr 52, 394-402 (2019)");
log<<plumed.cite("Niebling, Björling, Westenhoff, J. Appl. Crystallogr., 47, 1190–1198 (2014)");
log<<plumed.cite("Paissoni, Jussupow, Camilloni, J. Appl. Crystallogr., 52, 394-402 (2019)");
}
if(atomistic) {
log<<plumed.cite("Fraser, MacRae, Suzuki, J. Appl. Crystallogr., 11, 693–694 (1978)");
log<<plumed.cite("Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography C, 554–595 (International Union of Crystallography, 2006)");
log<<plumed.cite("Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography, C, 554–595 (International Union of Crystallography, 2006)");
}
if(resolution) {
log<<plumed.cite("Pedersen, Posselt, Mortensen, J. Appl. Crystallogr., 23, 321–333 (1990)");
Expand Down Expand Up @@ -1507,9 +1544,6 @@ unsigned SAXS::getOnebeadMapping(const PDB &pdb, const std::vector<AtomNumber> &
std::vector<std::string> chains; pdb.getChainNames( chains );
std::vector<std::vector<std::string> > AtomResidueName;

atoms_masses.resize(atoms.size());
residue_atom.resize(atoms.size());

// cycle over chains
for(unsigned i=0; i<chains.size(); ++i) {
unsigned start, end;
Expand All @@ -1521,8 +1555,7 @@ unsigned SAXS::getOnebeadMapping(const PDB &pdb, const std::vector<AtomNumber> &
std::string Rname = pdb.getResidueName(res, chains[i]);
Rname.erase(std::remove_if(Rname.begin(), Rname.end(), ::isspace),Rname.end());
std::vector<AtomNumber> res_atoms = pdb.getAtomsInResidue(res, chains[i]);
unsigned first_time=1;
std::vector<std::vector<unsigned> > tmp_residue_atom; tmp_residue_atom.resize(3);
std::vector<unsigned> tmp_residue_atom; tmp_residue_atom.resize(3,0);
// cycle over atoms
for(unsigned a=0; a<res_atoms.size(); a++) {
// operations shared among all beads
Expand All @@ -1538,21 +1571,17 @@ unsigned SAXS::getOnebeadMapping(const PDB &pdb, const std::vector<AtomNumber> &
} else {
type = Aname.at(1);
}
if (type == 'H') atoms_masses[res_atoms[a].index()] = 1.008;
else if(type == 'C') atoms_masses[res_atoms[a].index()] = 12.011;
else if(type == 'N') atoms_masses[res_atoms[a].index()] = 14.007;
else if(type == 'O') atoms_masses[res_atoms[a].index()] = 15.999;
else if(type == 'S') atoms_masses[res_atoms[a].index()] = 32.065;
else if(type == 'P') atoms_masses[res_atoms[a].index()] = 30.974;
if (type == 'H') atoms_masses.push_back(1.008);
else if(type == 'C') atoms_masses.push_back(12.011);
else if(type == 'N') atoms_masses.push_back(14.007);
else if(type == 'O') atoms_masses.push_back(15.999);
else if(type == 'S') atoms_masses.push_back(32.065);
else if(type == 'P') atoms_masses.push_back(30.974);
else {
error("Unknown element in mass extraction\n");
}
if(pdb.allowedResidue("protein",Rname)) {
if(first_time) {
atoms_per_bead.push_back(res_atoms.size());
first_time = 0;
}
residue_atom[res_atoms[a].index()] = atoms_per_bead.size()-1;
residue_atom.push_back(atoms_per_bead.size());
} else {
// check for nucleic acids
// Pentose bead
Expand All @@ -1562,7 +1591,8 @@ unsigned SAXS::getOnebeadMapping(const PDB &pdb, const std::vector<AtomNumber> &
Aname=="H2'2" || Aname=="H1'" || Aname=="HO5'" || Aname=="HO3'" || Aname=="HO2'" ||
Aname=="H5'1" || Aname=="H5'2" || Aname=="HO'2" || Aname=="H2'1" || Aname=="H5T" ||
Aname=="H3T" ) {
tmp_residue_atom[0].push_back(res_atoms[a].index());
residue_atom.push_back(atoms_per_bead.size()+0);
tmp_residue_atom[0]++;
}
// Nucleobase bead
else if(Aname=="N1" || Aname=="N2" || Aname=="N3" || Aname=="N4" || Aname=="N6" ||
Expand All @@ -1572,26 +1602,25 @@ unsigned SAXS::getOnebeadMapping(const PDB &pdb, const std::vector<AtomNumber> &
Aname=="H6" || Aname=="H8" || Aname=="H21" || Aname=="H22" || Aname=="H41" ||
Aname=="H42" || Aname=="H61" || Aname=="H62" || Aname=="H71" || Aname=="H72" ||
Aname=="H73" ) {
tmp_residue_atom[1].push_back(res_atoms[a].index());
residue_atom.push_back(atoms_per_bead.size()+1);
tmp_residue_atom[1]++;
}
// PO2 bead
else if(Aname=="P" || Aname=="OP1" || Aname=="OP2" || Aname=="OP3" || Aname=="O1P" ||
Aname=="O2P" || Aname=="O3P" ) {
tmp_residue_atom[2].push_back(res_atoms[a].index());
residue_atom.push_back(atoms_per_bead.size()+2);
tmp_residue_atom[2]++;
}
// error
else error("Atom name "+Aname+" cannot be indexed to any bead. Check the PDB.");
}
}
if(!pdb.allowedResidue("protein",Rname)) {
atoms_per_bead.push_back(tmp_residue_atom[0].size());
for(unsigned tmp_i=0; tmp_i<tmp_residue_atom[0].size(); tmp_i++) residue_atom[tmp_residue_atom[0][tmp_i]]=atoms_per_bead.size()-1;
atoms_per_bead.push_back(tmp_residue_atom[1].size());
for(unsigned tmp_i=0; tmp_i<tmp_residue_atom[1].size(); tmp_i++) residue_atom[tmp_residue_atom[1][tmp_i]]=atoms_per_bead.size()-1;
if(tmp_residue_atom[2].size()>0) {
atoms_per_bead.push_back(tmp_residue_atom[2].size());
for(unsigned tmp_i=0; tmp_i<tmp_residue_atom[2].size(); tmp_i++) residue_atom[tmp_residue_atom[2][tmp_i]]=atoms_per_bead.size()-1;
}
if(pdb.allowedResidue("protein",Rname)) {
atoms_per_bead.push_back(res_atoms.size());
} else {
atoms_per_bead.push_back(tmp_residue_atom[0]);
atoms_per_bead.push_back(tmp_residue_atom[1]);
if(tmp_residue_atom[2]>0) atoms_per_bead.push_back(tmp_residue_atom[2]);
}
}
}
Expand Down Expand Up @@ -3058,6 +3087,14 @@ void SAXS::getOnebeadparam(const PDB &pdb, const std::vector<AtomNumber> &atoms,
parameter_solv[CYS].push_back(-27885.23426006181);
parameter_solv[CYS].push_back(6280.15058191397);

parameter_solv[CYX].push_back(10281.960000119348);
parameter_solv[CYX].push_back(-42.315998754511);
parameter_solv[CYX].push_back(-19328.174487327480);
parameter_solv[CYX].push_back(-5523.191775626829);
parameter_solv[CYX].push_back(38185.463172673335);
parameter_solv[CYX].push_back(-28940.174693042034);
parameter_solv[CYX].push_back(6925.390014187676);

parameter_solv[ASP].push_back(13511.73760011933);
parameter_solv[ASP].push_back(-59.929111107656595);
parameter_solv[ASP].push_back(-25849.869639655575);
Expand Down Expand Up @@ -3226,6 +3263,14 @@ void SAXS::getOnebeadparam(const PDB &pdb, const std::vector<AtomNumber> &atoms,
parameter_mix[CYS].push_back(-18024.826330595406);
parameter_mix[CYS].push_back(3551.2207387570024);

parameter_mix[CYX].push_back(10746.617793719070);
parameter_mix[CYX].push_back(-37.082746200650);
parameter_mix[CYX].push_back(-17871.552278655203);
parameter_mix[CYX].push_back(-4512.203184574789);
parameter_mix[CYX].push_back(30605.726711712588);
parameter_mix[CYX].push_back(-21530.684072275839);
parameter_mix[CYX].push_back(4694.601090758420);

parameter_mix[ASP].push_back(13713.858501879382);
parameter_mix[ASP].push_back(-51.33286241257164);
parameter_mix[ASP].push_back(-23807.8549764091);
Expand Down Expand Up @@ -3394,6 +3439,14 @@ void SAXS::getOnebeadparam(const PDB &pdb, const std::vector<AtomNumber> &atoms,
parameter_vac[CYS].push_back(-2537.87137720241);
parameter_vac[CYS].push_back(381.52870758240016);

parameter_vac[CYX].push_back(2808.068549348085);
parameter_vac[CYX].push_back(-7.372260063948);
parameter_vac[CYX].push_back(-4017.492317531980);
parameter_vac[CYX].push_back(-840.151815748375);
parameter_vac[CYX].push_back(5800.074437790741);
parameter_vac[CYX].push_back(-3637.868824045027);
parameter_vac[CYX].push_back(659.528934122407);

parameter_vac[ASP].push_back(3479.750728224898);
parameter_vac[ASP].push_back(-10.33897891836596);
parameter_vac[ASP].push_back(-5382.628188436401);
Expand Down Expand Up @@ -3810,6 +3863,8 @@ void SAXS::getOnebeadparam(const PDB &pdb, const std::vector<AtomNumber> &atoms,
atoi[residue_atom[i]]=ASP;
} else if(Rname=="CYS") {
atoi[residue_atom[i]]=CYS;
} else if(Rname=="CYX") {
atoi[residue_atom[i]]=CYX;
} else if(Rname=="GLN") {
atoi[residue_atom[i]]=GLN;
} else if(Rname=="GLU") {
Expand Down Expand Up @@ -4317,6 +4372,14 @@ void SAXS::getOnebeadparam_sansH(const PDB &pdb, const std::vector<AtomNumber> &
parameter_solv_H[CYS].push_back(-27885.22747486708);
parameter_solv_H[CYS].push_back(6280.148346561226);

parameter_solv_H[CYX].push_back(10281.960000119348);
parameter_solv_H[CYX].push_back(-42.315998754511);
parameter_solv_H[CYX].push_back(-19328.174487327480);
parameter_solv_H[CYX].push_back(-5523.191775626829);
parameter_solv_H[CYX].push_back(38185.463172673335);
parameter_solv_H[CYX].push_back(-28940.174693042034);
parameter_solv_H[CYX].push_back(6925.390014187676);

parameter_solv_H[ASP].push_back(13511.73760011933);
parameter_solv_H[ASP].push_back(-59.92934247210642);
parameter_solv_H[ASP].push_back(-25849.867077822244);
Expand Down Expand Up @@ -4485,6 +4548,14 @@ void SAXS::getOnebeadparam_sansH(const PDB &pdb, const std::vector<AtomNumber> &
parameter_mix_H[CYS].push_back(-407.87897719750896);
parameter_mix_H[CYS].push_back(76.50541508448237);

parameter_mix_H[CYX].push_back(466.237200119199);
parameter_mix_H[CYX].push_back(-1.302082362010);
parameter_mix_H[CYX].push_back(-667.565738985901);
parameter_mix_H[CYX].push_back(-159.506437978088);
parameter_mix_H[CYX].push_back(1085.648159448292);
parameter_mix_H[CYX].push_back(-767.622943338598);
parameter_mix_H[CYX].push_back(170.157274620163);

parameter_mix_H[ASP].push_back(893.6531201192147);
parameter_mix_H[ASP].push_back(-3.0756255172248874);
parameter_mix_H[ASP].push_back(-1453.1760425275006);
Expand Down Expand Up @@ -4596,6 +4667,7 @@ void SAXS::getOnebeadparam_sansH(const PDB &pdb, const std::vector<AtomNumber> &
parameter_mix_H[HIS].push_back(5821.6258431396);
parameter_mix_H[HIS].push_back(-4415.32722209556);
parameter_mix_H[HIS].push_back(1044.7044029209756);

parameter_vac_H[TRP].push_back(36.42122511920832);
parameter_vac_H[TRP].push_back(-0.36925500341767903);
parameter_vac_H[TRP].push_back(-51.34228792835503);
Expand Down Expand Up @@ -4652,6 +4724,14 @@ void SAXS::getOnebeadparam_sansH(const PDB &pdb, const std::vector<AtomNumber> &
parameter_vac_H[CYS].push_back(2.3947518943233117);
parameter_vac_H[CYS].push_back(-0.40204949737133333);

parameter_vac_H[CYX].push_back(5.285401118868);
parameter_vac_H[CYX].push_back(-0.006119528779);
parameter_vac_H[CYX].push_back(-3.091212256902);
parameter_vac_H[CYX].push_back(-0.679948780910);
parameter_vac_H[CYX].push_back(4.495837313271);
parameter_vac_H[CYX].push_back(-2.827133444940);
parameter_vac_H[CYX].push_back(0.494583310914);

parameter_vac_H[ASP].push_back(14.776336119209605);
parameter_vac_H[ASP].push_back(-0.037351220316916435);
parameter_vac_H[ASP].push_back(-18.556358387626286);
Expand Down Expand Up @@ -5069,6 +5149,8 @@ void SAXS::getOnebeadparam_sansH(const PDB &pdb, const std::vector<AtomNumber> &
atoi[residue_atom[i]]=ASP;
} else if(Rname=="CYS") {
atoi[residue_atom[i]]=CYS;
} else if(Rname=="CYX") {
atoi[residue_atom[i]]=CYX;
} else if(Rname=="GLN") {
atoi[residue_atom[i]]=GLN;
} else if(Rname=="GLU") {
Expand Down Expand Up @@ -5576,6 +5658,14 @@ void SAXS::getOnebeadparam_sansD(const PDB &pdb, const std::vector<AtomNumber> &
parameter_mix_D[CYS].push_back(-1798.3157146799638);
parameter_mix_D[CYS].push_back(314.568167888235);

parameter_mix_D[CYX].push_back(1310.696400119220);
parameter_mix_D[CYX].push_back(-2.919852579787);
parameter_mix_D[CYX].push_back(-1902.283026713150);
parameter_mix_D[CYX].push_back(-340.431267947190);
parameter_mix_D[CYX].push_back(2480.025274590502);
parameter_mix_D[CYX].push_back(-1529.188197179144);
parameter_mix_D[CYX].push_back(278.926068515295);

parameter_mix_D[ASP].push_back(1861.6998401191709);
parameter_mix_D[ASP].push_back(-5.349780637260551);
parameter_mix_D[ASP].push_back(-2960.36741510377);
Expand Down Expand Up @@ -5744,6 +5834,14 @@ void SAXS::getOnebeadparam_sansD(const PDB &pdb, const std::vector<AtomNumber> &
parameter_vac_D[CYS].push_back(-17.248208429078456);
parameter_vac_D[CYS].push_back(1.0736187172140528);

parameter_vac_D[CYX].push_back(41.770369115535);
parameter_vac_D[CYX].push_back(-0.019277246931);
parameter_vac_D[CYX].push_back(-40.006821199463);
parameter_vac_D[CYX].push_back(-2.056736901533);
parameter_vac_D[CYX].push_back(23.707430747544);
parameter_vac_D[CYX].push_back(-8.010813092204);
parameter_vac_D[CYX].push_back(-0.023482540763);

parameter_vac_D[ASP].push_back(64.12806411920792);
parameter_vac_D[ASP].push_back(-0.08245818875074411);
parameter_vac_D[ASP].push_back(-78.95500211069523);
Expand Down Expand Up @@ -6064,6 +6162,8 @@ void SAXS::getOnebeadparam_sansD(const PDB &pdb, const std::vector<AtomNumber> &
atoi[residue_atom[i]]=ASP;
} else if(Rname=="CYS") {
atoi[residue_atom[i]]=CYS;
} else if(Rname=="CYX") {
atoi[residue_atom[i]]=CYX;
} else if(Rname=="GLN") {
atoi[residue_atom[i]]=GLN;
} else if(Rname=="GLU") {
Expand Down Expand Up @@ -6766,6 +6866,18 @@ std::map<std::string, std::vector<double> > SAXS::setupLCPOparam() {
lcpomap["CYS_OT2"] = { 1.6, 0.68563, -0.1868, -0.00135573, 0.00023743};
lcpomap["CYS_OXT"] = { 1.6, 0.88857, -0.33421, -0.0018683, 0.00049372};

lcpomap["CYX_N"] = { 1.65, 0.41102, -0.12254, -7.5448e-05, 0.00011804};
lcpomap["CYX_CA"] = { 1.7, 0.23348, -0.072627, -0.00020079, 7.967e-05};
lcpomap["CYX_C"] = { 1.7, 0.070344, -0.019015, -2.2009e-05, 1.6875e-05};
lcpomap["CYX_O"] = { 1.6, 0.68563, -0.1868, -0.00135573, 0.00023743};
lcpomap["CYX_CB"] = { 1.7, 0.56482, -0.19608, -0.0010219, 0.0002658};
lcpomap["CYX_SG"] = { 1.9, 0.54581, -0.19477, -0.0012873, 0.00029247};
lcpomap["CYX_OC1"] = { 1.6, 0.88857, -0.33421, -0.0018683, 0.00049372};
lcpomap["CYX_OC2"] = { 1.6, 0.68563, -0.1868, -0.00135573, 0.00023743};
lcpomap["CYX_OT1"] = { 1.6, 0.88857, -0.33421, -0.0018683, 0.00049372};
lcpomap["CYX_OT2"] = { 1.6, 0.68563, -0.1868, -0.00135573, 0.00023743};
lcpomap["CYX_OXT"] = { 1.6, 0.88857, -0.33421, -0.0018683, 0.00049372};

lcpomap["GLU_N"] = { 1.65, 0.41102, -0.12254, -7.5448e-05, 0.00011804};
lcpomap["GLU_CA"] = { 1.7, 0.23348, -0.072627, -0.00020079, 7.967e-05};
lcpomap["GLU_C"] = { 1.7, 0.070344, -0.019015, -2.2009e-05, 1.6875e-05};
Expand Down

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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.tmp
Found broken examples in automatic/Q3.tmp
Found broken examples in automatic/Q4.tmp
Found broken examples in automatic/Q6.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_LINEAR_PROJ.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_MAHA_DIST.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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