---------- Forwarded message ---------- From: James Jack <james.j...@symyx.com> Date: 2009/10/14 Subject: RE: [Noel O'Blog] New comment on Mono, C# and OpenBabel. To: Noel O'Boyle <baoille...@gmail.com>
Hi Noel,
I'm seeing a few issues preparing Cartesian MOPAC files from Molfiles
for certain structures.
I'm trying to take a 2D molfile and use OpenBabel to prepare a
Cartesian mop file suitable to send to MOPAC for geometrical
optimization.
See attached molfiles:
//Input.mol = my starting point
//Stage1.mol = openbabel reads in input.mol:
OBConversion obconv = new OBConversion();
OBMol mol = new OBMol();
string inputMolfileString = this.renditor1.MolfileString;
//set the MOPAC application location
MOPACPath = @"C:\Program Files\MOPAC\mopac2009.exe";
//convert to cartesian MOP
obconv.SetInFormat("mdl");
obconv.ReadString(mol, inputMolfileString);
//check the files is read in ok
obconv.SetOutFormat("mdl");
this.renderer1.MolfileString = obconv.WriteString(mol);
//result looks good
//stage2.mol
if (mol.GetDimension() < 3) //if we have a 2D structure
- prep for sending to MOPAC
{
//Generate a reasonable 3D model
OBOp builder = OBOp.FindType("Gen3D");
builder.Do(mol);
//check the resilt
obconv.SetOutFormat("mdl");
this.renderer1.MolfileString =
obconv.WriteString(mol); //looks bad - Nitrogens have valencies
overfilled
}
Currently things seem to go wrong at stage 2. Even if I do an
AddHydrogens() first the builder.Do(mol) seems to add extra H to the
nitrogens and I believe this causes issues later. For sure, if I
bypass stage2 by starting with a 3d molfile I get a much better
outcome.
I tried to replace stage2 as follows:
//Sprout H
mol.AddHydrogens();
//PreOptimize
OBForceField obff = OBForceField.FindForceField("MMFF94");
if (obff.Setup(mol))
{
obff.SteepestDescent(50);
if (obff.GetCoordinates(mol))
{
//check the output - we never get here - the
optimization/setup fails.
obconv.SetOutFormat("mdl");
this.renderer1.MolfileString = obconv.WriteString(mol);
}
}
But the preoptimize code fails, not sure why... Even if I pass it a
good 3D structure it still fails.
If you have any ideas I'd be interested to hear...
Best Regards,
James
--------------------------------------------------------------------------------
J. James Jack, Ph.D. +44 (0) 1530 220906, office
Senior Consultant +44 (0) 7834 215542, mobile
ELN Application Services +44 (0) 7590 258058, iPhone
Symyx Technologies UK ltd. james.j...@symyx.com
www.symyx.com
--------------------------------------------------------------------------------
stage2.mol
Description: Binary data
input.mol
Description: Binary data
stage1.mol
Description: Binary data
mopac output.mol
Description: Binary data
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