public static CTestgrad Testgrad(string testgradpath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // = null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTestgrad testgrad;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testgradpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "testgrad.exe", "testgrad.exe");
testgradpath = "testgrad.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if (keys != null && keys.Length > 0)
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testgrad = TestgradImpl(testgradpath, "test.xyz", "test.prm", keypath, optOutSource);
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(testgrad);
}
public static CTesthess Testhess
(string testhesspath
, Tinker.Xyz xyz
, Tinker.Prm prm
, string tempbase //=null
, string[] keys
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
CTesthess testhess;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
if (testhesspath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_01.";
HResource.CopyResourceTo <Tinker>(resbase + "testhess.exe", "testhess.exe");
testhesspath = "testhess.exe";
}
xyz.ToFile("test.xyz", false);
prm.ToFile("test.prm");
string keypath = null;
if ((keys != null) && (keys.Length > 0))
{
keypath = "test.key";
HFile.WriteAllLines(keypath, keys);
}
testhess = Testhess(testhesspath, "test.xyz", "test.prm", keypath, optOutSource, HessMatrixZeros);
testhess.xyz = xyz;
testhess.prm = prm;
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
string test_eig = "true";
if (test_eig == "false")
{
Vector D;
using (new Matlab.NamedLock(""))
{
Matlab.PutSparseMatrix("testeig.H", testhess.hess.GetMatrixSparse(), 3, 3);
Matlab.Execute("testeig.H = (testeig.H + testeig.H')/2;");
Matlab.Execute("[testeig.V, testeig.D] = eig(full(testeig.H));");
Matlab.Execute("testeig.D = diag(testeig.D);");
D = Matlab.GetVector("testeig.D");
Matlab.Execute("clear testeig;");
}
}
return(testhess);
}
public static CPsfgen Psfgen
(IList <Tuple <string, string, Pdb.IAtom[]> > lstSegFileAtoms // segname, filename, pdbatoms
, string tempbase //=null
, string parameters //=null
, string namdversion //="2.8"
, IList <string> infiles
, IList <string> outfiles
, string topology
, IList <string> psfgen_lines = null
, string psfgen_workdir = null
, HOptions options = null
)
{
if (options == null)
{
options = new HOptions((string)null);
}
Dictionary <System.IO.FileInfo, string[]> infile_lines = new Dictionary <System.IO.FileInfo, string[]>();
foreach (string infile in infiles)
{
infile_lines.Add(HFile.GetFileInfo(infile), HFile.ReadAllLines(infile));
}
string currpath = HEnvironment.CurrentDirectory;
System.IO.DirectoryInfo tmpdir = null;
if (psfgen_workdir != null)
{
HEnvironment.CurrentDirectory = psfgen_workdir;
}
else
{
tmpdir = HDirectory.CreateTempDirectory(tempbase);
HEnvironment.CurrentDirectory = tmpdir.FullName;
}
string[] lines = null;
if ((psfgen_lines != null) && (psfgen_lines.Count > 0))
{
lines = psfgen_lines.ToArray();
}
else
{
lines = GetPsfgenLines
(custom_pdbalias: null
, custom_patches: null
);
}
if (topology != null)
{
lines = lines.ToArray().HReplace("$topology$", topology);
}
List <string> psf_lines;
List <string> pdb_lines;
{
{
//foreach(var respath_filename in GetResourcePaths("2.8", "psfgen"))
foreach (var respath_filename in GetResourcePaths(namdversion, "psfgen"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
// Dictionary<string, Tuple<string, Pdb.IAtom[]>> segname_filename_pdbatoms = new Dictionary<string, Tuple<string, Pdb.IAtom[]>>();
// //if(pdbs.Length != 1) throw new ArgumentException();
// for(int i=0; i<lstSegFilePdb.Count; i++)
// {
// string segnameprefix = lstSegFilePdb[i].Item1; if( segnameprefix == null) segnameprefix = string.Format("{0:00}", i);
// string filenameprefix = lstSegFilePdb[i].Item2; if(filenameprefix == null) filenameprefix = string.Format("{0:00}", i);
// Pdb pdb = lstSegFilePdb[i].Item3;
// List<Pdb.IAtom> pdb_atoms = new List<Pdb.IAtom>();
// pdb_atoms.AddRange(pdb.atoms);
// pdb_atoms.AddRange(pdb.hetatms);
// char[] chains = pdb_atoms.ListChainID().HToHashSet().ToArray();
//
// HDebug.AssertIf(chains.Length> 1, segnameprefix.Length <= 5);
// HDebug.AssertIf(chains.Length<=1, segnameprefix.Length <= 6);
// foreach(char chain in chains)
// {
// Pdb.IAtom[] chain_atoms = pdb_atoms.SelectByChainID(chain).SelectByAltLoc().ToArray();
// string suffix = null;
// if(('a' <= chain) && (chain <= 'z')) suffix = string.Format("L{0}", chain);
// if(('A' <= chain) && (chain <= 'Z')) suffix = string.Format("U{0}", chain);
// if(('0' <= chain) && (chain <= '9')) suffix = string.Format("N{0}", chain);
// string segname = segnameprefix + ((chains.Length <= 1) ? "" : suffix);
// string filename = filenameprefix + ((chains.Length <= 1) ? "" : suffix);
// segname_filename_pdbatoms.Add(segname, new Tuple<string,Pdb.IAtom[]>(filename, chain_atoms));
// }
// }
foreach (var finfo_line in infile_lines)
{
string inname = finfo_line.Key.Name;
string[] inlines = finfo_line.Value;
HFile.WriteAllLines(inname, inlines);
}
HashSet <string> segnames = new HashSet <string>();
int segindex = 0;
foreach (var seg_file_atoms in lstSegFileAtoms)
{
string segname = seg_file_atoms.Item1;
string filename = seg_file_atoms.Item2;
Pdb.IAtom[] chain_atoms = seg_file_atoms.Item3.SelectByAltLoc().ToArray();
HDebug.Exception(chain_atoms.ListChainID().HToHashSet().Count == 1);
if (segname == null)
{
while (segindex <= 9999)
{
if (segnames.Contains(segindex.ToString()) == false)
{
segname = segindex.ToString();
segnames.Add(segname);
break;
}
segindex++;
}
}
if (filename == null)
{
filename = segname;
}
Pdb.ToFile
(filename + ".pdb"
, chain_atoms.HToType <Pdb.IAtom, Pdb.Element>()
, false
);
for (int i = 0; i < lines.Length; i++)
{
if (lines[i].Contains("$segname$"))
{
string insert = lines[i];
insert = insert.Replace("$segname$", segname);
insert = insert.Replace("$segfilename$", filename);
lines = lines.HInsert(i, insert);
i++;
}
}
}
lines = lines.HRemoveAllContains("$segname$");
HFile.WriteAllLines("prot.inp", lines);
string command0 = string.Format("psfgen < prot.inp");
bool pause = options.Contains("psfgen pause");
HProcess.StartAsBatchInConsole(null, pause, command0);
psf_lines = System.IO.File.ReadLines("prot.psf").ToList();
pdb_lines = System.IO.File.ReadLines("prot.pdb").ToList();
}
HEnvironment.CurrentDirectory = currpath;
if (tmpdir != null)
{
try{ tmpdir.Delete(true); } catch {}
}
return(new CPsfgen
{
psf_lines = psf_lines,
pdb_lines = pdb_lines,
});
}
public static CPdbxyz Pdbxyz
(Pdb pdb
, Tinker.Prm prm
, string tempbase //=null
, string parameters //=null
, string tinkerversion //="6.2.1"
, params string[] keys
)
{
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
Tinker.Xyz xyz;
string[] seq;
string[] capture;
{
HEnvironment.CurrentDirectory = tmpdir.FullName;
{
foreach (var respath_filename in GetResourcePaths("6.2.1", "pdbxyz"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
pdb.ToFile("prot.pdb");
prm.ToFile("prot.prm");
string keypath = null;
if ((keys != null) && (keys.Length > 0))
{
keypath = "prot.key";
HFile.WriteAllLines(keypath, keys);
}
{
//bool ComputeAnalyticalGradientVector = true;
//bool ComputeNumericalGradientVector = false;
//bool OutputBreakdownByGradientComponent = false;
string command = "";
command += "pdbxyz.exe";
command += " prot.pdb";
command += " prot.prm";
if (keypath != null)
{
command += " -k " + keypath;
}
command += " > output.txt";
List <string> errors = new List <string>();
int exitcode = HProcess.StartAsBatchSilent(null, null, errors, command);
capture = HFile.ReadAllLines("output.txt");
capture = capture.HAddRange(errors.ToArray());
xyz = Tinker.Xyz.FromFile("prot.xyz", false);
if (HFile.Exists("prot.seq"))
{
seq = HFile.ReadAllLines("prot.seq");
}
else
{
seq = null;
}
}
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
return(new CPdbxyz
{
xyz = xyz,
seq = seq,
capture = capture,
});
}
public static CNamd2 Namd2
(IList <string> pdb_lines
, IList <string> psf_lines
, IList <string> prm_lines
, string tempbase // = null
, string namd2version // = "2.8"
, string option // = "+p3"
, IList <string> infiles = null
, IList <string> outfiles = null
, IList <string> conf_lines = null
)
{
string[] lines = null;
if ((conf_lines != null) && (conf_lines.Count > 0))
{
lines = conf_lines.ToArray();
}
else
{
// http://www.msg.ucsf.edu/local/programs/Vega/pages/tu_namdmin.htm
lines = new string[]
{ "numsteps 10000 " // minimization steps
//{ "numsteps 1000 " // minimization steps
, "minimization on "
, "dielectric 1.0 "
, "coordinates prot.pdb " // coordinate file
, "outputname output " // output file: prot.coor
, "outputEnergies 1000 "
, "binaryoutput no "
, "DCDFreq 1000 "
, "restartFreq 1000 "
, "structure prot.psf " // psf file
, "paraTypeCharmm on "
, "parameters prot.prm " // parameter file
//, "parameters par_all22_vega.inp "
, "exclude scaled1-4 "
, "1-4scaling 1.0 "
, "switching on "
, "switchdist 8.0 "
, "cutoff 22.0 " //, "cutoff 12.0 "
, "pairlistdist 23.5 " //, "pairlistdist 13.5 "
, "margin 0.0 "
, "stepspercycle 20 "
, "fixedAtoms on " // fix atoms
, "fixedAtomsCol O " // select fixing atoms from O
};
}
var tmpdir = HDirectory.CreateTempDirectory(tempbase);
string currpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = tmpdir.FullName;
string[] coor_lines = null;
double coor_rmsd = double.NaN;
{
{
//foreach(var respath_filename in GetResourcePaths("2.8", "psfgen"))
foreach (var respath_filename in GetResourcePaths(namd2version, "namd2"))
{
string respath = respath_filename.Item1;
string filename = respath_filename.Item2;
HResource.CopyResourceTo <Tinker>(respath, filename);
}
}
Vector[] coords0 = Pdb.FromLines(pdb_lines).atoms.ListCoord().ToArray();
System.IO.File.WriteAllLines("prot.pdb", pdb_lines);
System.IO.File.WriteAllLines("prot.psf", psf_lines);
System.IO.File.WriteAllLines("prot.prm", prm_lines);
System.IO.File.WriteAllLines("prot.conf", lines);
if (option == null)
{
option = "";
}
string command = string.Format("namd2 {0} prot.conf", option);
HProcess.StartAsBatchInConsole(null, false, command);
if (HFile.Exists("output.coor"))
{
coor_lines = HFile.ReadAllLines("output.coor");
Vector[] coords1 = Pdb.FromLines(coor_lines).atoms.ListCoord().ToArray();
Vector[] coords1x = Align.MinRMSD.Align(coords0, coords1);
coor_rmsd = Align.MinRMSD.GetRMSD(coords0, coords1x);
}
}
HEnvironment.CurrentDirectory = currpath;
try{ tmpdir.Delete(true); } catch {}
if (coor_lines == null)
{
return(null);
}
return(new CNamd2
{
coor_lines = coor_lines,
coor_rmsd = coor_rmsd,
});
}
public static ONewton Newton(string tinkerpath
, Tinker.Xyz xyz
, Tinker.Xyz.Atom.Format xyz_atoms_format
, Tinker.Prm prm
, string tempbase
, string copytemp // = null
, string param
//, string precondition // = "A" // Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
//, double gradCriterion // = 0.01 // Enter RMS Gradient per Atom Criterion [0.01] : 0.001
, IList <Tinker.Xyz.Atom> atomsToFix // = null
, bool pause // = false
, params string[] keys
)
{
if (HDebug.IsDebuggerAttached && atomsToFix != null)
{
Dictionary <int, Tinker.Xyz.Atom> xyzatoms = xyz.atoms.ToIdDictionary();
foreach (var atom in atomsToFix)
{
HDebug.Assert(object.ReferenceEquals(atom, xyzatoms[atom.Id]));
}
}
Tinker.Xyz minxyz;
string[] minlog;
using (var temp = new HTempDirectory(tempbase, copytemp))
{
temp.EnterTemp();
if (tinkerpath == null)
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.tinker_6_2_06.";
HResource.CopyResourceTo <Tinker>(resbase + "newton.exe", "newton.exe");
tinkerpath = "newton.exe";
}
xyz.ToFile("prot.xyz", false);
prm.ToFile("prot.prm");
List <string> keylines = new List <string>(keys);
if (atomsToFix != null)
{
foreach (var atom in atomsToFix)
{
Vector coord = atom.Coord;
double force_constant = 10000; // force constant in kcal/Å2 for the harmonic restraint potential
string keyline = string.Format("RESTRAIN-POSITION {0} {1} {2} {3} {4}", atom.Id, coord[0], coord[1], coord[2], force_constant);
keylines.Add(keyline);
}
}
HFile.WriteAllLines("prot.key", keylines);
// Precondition via Auto/None/Diag/Block/SSOR/ICCG [A] : A
// Enter RMS Gradient per Atom Criterion [0.01] : 0.001
//bool pause = false;
string command = tinkerpath;
command += string.Format(" prot.xyz prot.prm");
command += string.Format(" -k prot.key");
command += string.Format(" {0}", param);
HProcess.StartAsBatchInConsole("newton.bat", pause
, "time /t >> prot.log"
, command //+" >> prot.log"
, "time /t >> prot.log"
);
HDebug.Assert(HFile.Exists("prot.xyz_2"));
HDebug.Assert(HFile.Exists("prot.xyz_3") == false);
minxyz = Tinker.Xyz.FromFile("prot.xyz_2", false, xyz_atoms_format);
minlog = HFile.ReadAllLines("prot.log");
temp.QuitTemp();
}
return(new ONewton
{
minxyz = minxyz,
minlog = minlog
});
}
public static void SelfTest(string pdbname, string psfname, string prmname, string xyzname)
{
using (var temp = new HTempDirectory(@"C:\temp\", null))
{
temp.EnterTemp();
{
string resbase = "HTLib2.Bioinfo.HTLib2.Bioinfo.External.Tinker.Resources.selftest.";
HResource.CopyResourceTo <Tinker>(resbase + pdbname, pdbname);
HResource.CopyResourceTo <Tinker>(resbase + psfname, psfname);
HResource.CopyResourceTo <Tinker>(resbase + "par_all27_prot_lipid.inp", prmname);
if (xyzname != null)
{
HResource.CopyResourceTo <Tinker>(resbase + xyzname, xyzname);
}
HResource.CopyResourceTo <Tinker>(resbase + "charmm22.prm", "charmm22.prm");
{
var pdb = Pdb.FromFile(pdbname);
var psf = Namd.Psf.FromFile(psfname);
var prm = Namd.Prm.FromFile(prmname);
var xyz_prm = BuildFromNamd(pdb, psf, prm);
xyz_prm.Item1.ToFile("TinkFromNamd.xyz", false);
xyz_prm.Item2.ToFile("TinkFromNamd.prm");
}
if (xyzname != null)
{
var xyz0 = Xyz.FromFile("TinkFromNamd.xyz", false);
var prm0 = Prm.FromFile("TinkFromNamd.prm");
var grad0 = Run.Testgrad(xyz0, prm0, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc0 = grad0.anlyts.GetForces(xyz0.atoms);
var xyz1 = Xyz.FromFile(xyzname, false);
var prm1 = Prm.FromFile("charmm22.prm");
var grad1 = Run.Testgrad(xyz1, prm1, @"C:\temp\"
//, "VDWTERM NONE"
//, "CHARGETERM NONE"
//, "BONDTERM NONE"
//, "ANGLETERM NONE"
//, "UREYTERM NONE"
//, "IMPROPTERM NONE"
//, "TORSIONTERM NONE"
);
var forc1 = grad1.anlyts.GetForces(xyz1.atoms);
{
KDTree.KDTree <object> kdtree = new KDTree.KDTree <object>(3);
var atoms0 = xyz0.atoms;
for (int i = 0; i < atoms0.Length; i++)
{
kdtree.insert(atoms0[i].Coord, i);
}
var atoms1 = xyz1.atoms;
int[] idx1to0 = new int[atoms1.Length];
for (int i1 = 0; i1 < atoms1.Length; i1++)
{
Vector coord1 = atoms1[i1].Coord;
int i0 = (int)kdtree.nearest(coord1);
Vector coord0 = atoms0[i0].Coord;
kdtree.delete(coord0);
idx1to0[i0] = i1;
}
atoms1 = atoms1.HSelectByIndex(idx1to0);
forc1 = forc1.HSelectByIndex(idx1to0);
}
Vector[] dforc = VectorBlock.PwSub(forc0, forc1).ToArray();
double[] dforcl = dforc.Dist();
double max_dforc = dforc.Dist().Max();
HDebug.Exception(max_dforc < 1); // 0.72682794387667848
{
double EB = Math.Abs(grad0.enrgCmpnt.EB - grad1.enrgCmpnt.EB); HDebug.Exception(EB < 0.1);
double EA = Math.Abs(grad0.enrgCmpnt.EA - grad1.enrgCmpnt.EA); HDebug.Exception(EA < 0.1);
double EBA = Math.Abs(grad0.enrgCmpnt.EBA - grad1.enrgCmpnt.EBA); HDebug.Exception(EBA < 0.1);
double EUB = Math.Abs(grad0.enrgCmpnt.EUB - grad1.enrgCmpnt.EUB); HDebug.Exception(EUB < 0.1);
double EAA = Math.Abs(grad0.enrgCmpnt.EAA - grad1.enrgCmpnt.EAA); HDebug.Exception(EAA < 0.1);
double EOPB = Math.Abs(grad0.enrgCmpnt.EOPB - grad1.enrgCmpnt.EOPB); HDebug.Exception(EOPB < 0.1);
double EOPD = Math.Abs(grad0.enrgCmpnt.EOPD - grad1.enrgCmpnt.EOPD); HDebug.Exception(EOPD < 0.1);
double EID = Math.Abs(grad0.enrgCmpnt.EID - grad1.enrgCmpnt.EID); HDebug.Exception(EID < 0.1); // 0.0019000000000000128 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EIT = Math.Abs(grad0.enrgCmpnt.EIT - grad1.enrgCmpnt.EIT); HDebug.Exception(EIT < 0.1);
double ET = Math.Abs(grad0.enrgCmpnt.ET - grad1.enrgCmpnt.ET); HDebug.Exception(ET < 0.5); // 0.33029999999999404 : N-terminus (and C-terminus) information is/are inconsistent betweeen namd-charmm and tink-charmm22
double EPT = Math.Abs(grad0.enrgCmpnt.EPT - grad1.enrgCmpnt.EPT); HDebug.Exception(EPT < 0.1);
double EBT = Math.Abs(grad0.enrgCmpnt.EBT - grad1.enrgCmpnt.EBT); HDebug.Exception(EBT < 0.1);
double ETT = Math.Abs(grad0.enrgCmpnt.ETT - grad1.enrgCmpnt.ETT); HDebug.Exception(ETT < 0.1);
double EV = Math.Abs(grad0.enrgCmpnt.EV - grad1.enrgCmpnt.EV); HDebug.Exception(EV < 0.1);
double EC = Math.Abs(grad0.enrgCmpnt.EC - grad1.enrgCmpnt.EC); HDebug.Exception(EC < 0.5); // 0.37830000000002428
double ECD = Math.Abs(grad0.enrgCmpnt.ECD - grad1.enrgCmpnt.ECD); HDebug.Exception(ECD < 0.1);
double ED = Math.Abs(grad0.enrgCmpnt.ED - grad1.enrgCmpnt.ED); HDebug.Exception(ED < 0.1);
double EM = Math.Abs(grad0.enrgCmpnt.EM - grad1.enrgCmpnt.EM); HDebug.Exception(EM < 0.1);
double EP = Math.Abs(grad0.enrgCmpnt.EP - grad1.enrgCmpnt.EP); HDebug.Exception(EP < 0.1);
double ER = Math.Abs(grad0.enrgCmpnt.ER - grad1.enrgCmpnt.ER); HDebug.Exception(ER < 0.1);
double ES = Math.Abs(grad0.enrgCmpnt.ES - grad1.enrgCmpnt.ES); HDebug.Exception(ES < 0.1);
double ELF = Math.Abs(grad0.enrgCmpnt.ELF - grad1.enrgCmpnt.ELF); HDebug.Exception(ELF < 0.1);
double EG = Math.Abs(grad0.enrgCmpnt.EG - grad1.enrgCmpnt.EG); HDebug.Exception(EG < 0.1);
double EX = Math.Abs(grad0.enrgCmpnt.EX - grad1.enrgCmpnt.EX); HDebug.Exception(EX < 0.1);
}
}
}
temp.QuitTemp();
}
//{
// //string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\New folder\";
// string pathbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\1A6G\";
// string toplbase = @"C:\Users\htna.IASTATE\svn\htnasvn_htna\Research.bioinfo.prog.NAMD\top_all27_prot_lipid\";
// var pdb = Pdb .FromFile(pathbase+"1A6G.psfgen.pdb");
// var psf = Namd.Psf.FromFile(pathbase+"1A6G.psfgen.psf");
// var prm = Namd.Prm.FromFile(toplbase+"par_all27_prot_na.prm");
//
// pdb = Pdb .FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.pdb");
// psf = Namd.Psf.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\1M6J.psfgen.psf");
// prm = Namd.Prm.FromFile(@"K:\Tim-8TIM,1TPH,1M6J\Tim-1M6J\par_all27_prot_lipid.inp");
// var xyz_prm = BuildFromNamd(pdb, psf, prm);
// xyz_prm.Item1.ToFile(@"C:\temp\TinkFromNamd.xyz", false);
// xyz_prm.Item2.ToFile(@"C:\temp\TinkFromNamd.prm");
//}
}