Пример #1
0
/** Sets the temporary charge array and makes sure that we have the necessary
  * parameters in our topology to calculate nonbonded energy terms
  */
int Action_LIE::SetupParms(Topology const& ParmIn) {
  if (!ParmIn.Nonbond().HasNonbond()) {
    mprinterr("Error: Topology does not have LJ information.\n");
    return 1;
  }
  // Store the charges
  atom_charge_.clear();
  atom_charge_.reserve( ParmIn.Natom() );
  for (Topology::atom_iterator atom = ParmIn.begin();
                               atom != ParmIn.end(); ++atom)
    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) );
  return 0;
}
Пример #2
0
/** Sets the temporary charge array and makes sure that we have the necessary
  * parameters in our topology to calculate nonbonded energy terms
  */
int Action_Spam::SetupParms(Topology* ParmIn) {
  // Store the charges
  atom_charge_.clear();
  atom_charge_.reserve( ParmIn->Natom() );
  for (Topology::atom_iterator atom = ParmIn->begin();
       atom != ParmIn->end(); ++atom)
    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER );
  if (!ParmIn->Nonbond().HasNonbond()) {
    mprinterr("Error: SPAM: Parm does not have LJ information.\n");
    return 1;
  }
  return 0;
}
Пример #3
0
int Analysis_Matrix::NMWizOutput() const {
  // Check # vecs
  int nvecs;
  if (nmwizvecs_ <= modes_->Nmodes())
    nvecs = nmwizvecs_;
  else {
    mprintf("Warning: nmwizvecs > # eigenvectors, only writing %i vecs.\n",
            modes_->Nmodes());
    nvecs = modes_->Nmodes();
  }
  // Check # atoms
  if (nmwizParm_.Natom() * 3 != modes_->VectorSize()) {
    mprinterr("Error: nmwiz topology size %i does not match eigenvector size %i.\n",
              nmwizParm_.Natom() * 3, modes_->VectorSize());
    return 1;
  }
  
  nmwizfile_->Printf("nmwiz_load %s\n", nmwizfile_->Filename().full());

  nmwizfile_->Printf("name default_name\n");  //TODO: get from optionally provided pdb file

  nmwizfile_->Printf("atomnames ");
  for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
        nmwizfile_->Printf("%s ", atom->c_str());
  nmwizfile_->Printf("\n");

  nmwizfile_->Printf("resnames ");
  for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
    nmwizfile_->Printf("%s ", nmwizParm_.Res(atom->ResNum()).c_str());
  nmwizfile_->Printf("\n");

  nmwizfile_->Printf("resids ");
  for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
    nmwizfile_->Printf("%d ", atom->ResNum()+1);
  nmwizfile_->Printf("\n");

  nmwizfile_->Printf("chainids \n");    //TODO: get from optionally provided pdb file

  nmwizfile_->Printf("bfactors \n");    //TODO: get from optionally provided pdb file

  nmwizfile_->Printf("coordinates ");
  for (int i = 0; i < modes_->NavgCrd(); ++i)
          nmwizfile_->Printf("%8.3f ", modes_->AvgCrd()[i]);
  nmwizfile_->Printf("\n");

  for (int vec = 0; vec < nvecs; ++vec){
    nmwizfile_->Printf("mode %i %12.10f ", vec+1, 1/modes_->Eigenvalue(vec));
    const double* Vec = modes_->Eigenvector(vec);
    for (int i = 0 ; i < modes_->VectorSize(); ++i)
      nmwizfile_->Printf("%12.5f ", Vec[i]);
    nmwizfile_->Printf("\n");
  }
  return 0;
}
Пример #4
0
int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
  // TODO: CMAP etc info
  CpptrajFile outfile;
  if (outfile.OpenWrite(fname)) return 1;
  // Write PSF
  outfile.Printf("PSF\n\n");
  // Write title
  std::string titleOut = parm.ParmName();
  titleOut.resize(78);
  outfile.Printf("%8i !NTITLE\n* %-78s\n\n", 1, titleOut.c_str());
  // Write NATOM section
  outfile.Printf("%8i !NATOM\n", parm.Natom());
  unsigned int idx = 1;
  // Make fake segment ids for now.
  char segid[2];
  segid[0] = 'A';
  segid[1] = '\0';
  mprintf("Warning: Assigning single letter segment IDs.\n");
  int currentMol = 0;
  bool inSolvent = false;
  for (Topology::atom_iterator atom = parm.begin(); atom != parm.end(); ++atom, ++idx) {
    int resnum = atom->ResNum();
    if (atom->MolNum() != currentMol) {
      if (!inSolvent) {
        inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
        currentMol = atom->MolNum();
        segid[0]++;
      } else
        inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
    }
    // TODO: Print type name for xplor-like PSF
    int typeindex = atom->TypeIndex() + 1;
    // If type begins with digit, assume charmm numbers were read as
    // type. Currently Amber types all begin with letters.
    if (isdigit(atom->Type()[0]))
      typeindex = convertToInteger( *(atom->Type()) );
    // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
    outfile.Printf("%8i %-4s %-4i %-4s %-4s %4i %14.6G %9g  %10i\n", idx, segid,
                   parm.Res(resnum).OriginalResNum(), parm.Res(resnum).c_str(),
                   atom->c_str(), typeindex, atom->Charge(),
                   atom->Mass(), 0);
  }
  outfile.Printf("\n");
  // Write NBOND section
  outfile.Printf("%8u !NBOND: bonds\n", parm.Bonds().size() + parm.BondsH().size());
  idx = 1;
  for (BondArray::const_iterator bond = parm.BondsH().begin();
                                 bond != parm.BondsH().end(); ++bond, ++idx)
  {
    outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
    if ((idx % 4)==0) outfile.Printf("\n"); 
  }
  for (BondArray::const_iterator bond = parm.Bonds().begin();
                                 bond != parm.Bonds().end(); ++bond, ++idx)
  {
    outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
    if ((idx % 4)==0) outfile.Printf("\n"); 
  }
  if ((idx % 4)!=0) outfile.Printf("\n");
  outfile.Printf("\n");
  // Write NTHETA section
  outfile.Printf("%8u !NTHETA: angles\n", parm.Angles().size() + parm.AnglesH().size());
  idx = 1;
  for (AngleArray::const_iterator ang = parm.AnglesH().begin();
                                  ang != parm.AnglesH().end(); ++ang, ++idx)
  {
    outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
    if ((idx % 3)==0) outfile.Printf("\n");
  }
  for (AngleArray::const_iterator ang = parm.Angles().begin();
                                  ang != parm.Angles().end(); ++ang, ++idx)
  {
    outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
    if ((idx % 3)==0) outfile.Printf("\n");
  }
  if ((idx % 3)==0) outfile.Printf("\n");
  outfile.Printf("\n");
  // Write out NPHI section
  outfile.Printf("%8u !NPHI: dihedrals\n", parm.Dihedrals().size() + parm.DihedralsH().size());
  idx = 1;
  for (DihedralArray::const_iterator dih = parm.DihedralsH().begin();
                                     dih != parm.DihedralsH().end(); ++dih, ++idx)
  {
    outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
    if ((idx % 2)==0) outfile.Printf("\n");
  }
  for (DihedralArray::const_iterator dih = parm.Dihedrals().begin();
                                     dih != parm.Dihedrals().end(); ++dih, ++idx)
  {
    outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
    if ((idx % 2)==0) outfile.Printf("\n");
  }
  if ((idx % 2)==0) outfile.Printf("\n");
  outfile.Printf("\n");

  outfile.CloseFile();
  return 0;
}