Problems using MarvinBeans.jar

Hi,

I am using MarvinBeans.jar in our project. While using I faced some problems that I am going to address them in the following:

 1- In the project I am using Molecule class. I want to add MolAtoms to this molecule but there is no method to add any MolAtoms to an object of Molecule class. What should I do?

 2- When I clone an object of MolAtom class I see that its bonds are not copied and the bondcount is zero. What should I do?

 3- The third question, which I was wondering if you could give me some suggestions, I am using DreidingFF class (which seem so useful for our project because if I was going to develope a class to calculate the potential energy of a molecule would take me so long). To use DreidingFF I have to use the format your Molecule class in the whole of my program. Is there any other way to use DreidingFF?

 I really appreciate your help,

 best regards,

Hooman Peiro Sajjad

Hi,

I would like to answer your third question:

Energy calculations from API can be done using Molecule.clean(3,...) method. A detailed list of clean3D options applicable can be obtained from molconverter command line tool by  "molconvert -H3D".

Calling m.clean(3,null) will generate 3D coordinates with default settings; m.clean(3,"E") will generate coordinates and store calculated energy in property "Energy", while m.clean(3,"c2E") will calculate energy using current coordinates.

For an example see attached source Energy.java.

If you have any further questions do not hesitate to ask them

Regards,

Gabor

Hi,

Please find my responds to the first two questions:

1- In the project I am using Molecule class. I want to add MolAtoms to this molecule but there is no method to add any MolAtoms to an object of Molecule class. What should I do?
The method CGraph.add(CNode node) adds a node to the graph.
You can call this method from the Molecule class with MolAtom parameter to add a MolAtom object to the Molecule object.

2- When I clone an object of MolAtom class I see that its bonds are not copied and the bondcount is zero. What should I do?
You can try to clone the whole Molecule object. (Unused part of the Molecule object can be removed by the remove methods of CGraph or Molecule class)

I hope this helps.

Regards,
Erika.

Thanks for your accurate response. I wanted to know the method that this energy is calculated by. Is it Dreiding force field?

Also imagine that I want to read the molecule from a file. then I want to modify the atoms coordinations each time. To do so I should do as following if I understand it well?:

MolAtom tempAtom = myMolecule.getAtom(someIndex);

TempAtom.setXYZ(x, y, z);

I really appreciate your support,

Hooman

Hi,

I wanted to know the method that this energy is calculated by. Is it Dreiding force field? 

Our force field is based on the Dreiding force field (S. L. Mayo, B. D. Olafson, W. A. Goddard III., J. Phys. Chem., 1990, 94, 8897-8909), however several modifications were introduced. 

Also imagine that I want to read the molecule

from a file. then I want to modify the atoms coordinations each time.

To do so I should do as following if I understand it well?:


MolAtom tempAtom = myMolecule.getAtom(someIndex);


TempAtom.setXYZ(x, y, z);

Yes, that will set the given 3D coordinates for that atom.

Regards,

Gabaor

Thanks for your help,

about question number 1 I think there won't be any problem and I should implement it and see whether I can use it or not. but about question number 2 I think for my implementation it is not appropriate to clone the whole molecule each time. For example I want to make 10 sample atoms of each atoms of the molecule and change their properties seperately, then it is not efficient to clone the whole atom for each of them. Do you have any idea what else I can do?

best best regards :)

Hooman

I wanted to know the method that this energy is calculated by. Is it Dreiding force field? 

Also imagine that I want to read the molecule

from a file. then I want to modify the atoms coordinations each time.

To do so I should do as following if I understand it well?:


MolAtom tempAtom = myMolecule.getAtom(someIndex);


TempAtom.setXYZ(x, y, z);

So cool,

The support given in this forum is awesome :)

I wanted to know the method that this energy is calculated by. Is it Dreiding force field? 

Also imagine that I want to read the molecule

from a file. then I want to modify the atoms coordinations each time.

To do so I should do as following if I understand it well?:


MolAtom tempAtom = myMolecule.getAtom(someIndex);


TempAtom.setXYZ(x, y, z);

Hi again,

I am using molecule.getProperty("Energy") to get the energy of the molecule. But for non bonded atoms it results zeroy. I wanted to know that in Dreiding energy, it does not calculate non bonded forces or it deos? for example for a molecule of two atoms which are not connected together, a complete force field model should calculate the non bonded energy.

regards regards

Hi,

I am using molecule.getProperty("Energy") to get

the energy of the molecule. But for non bonded atoms it results zeroy.

I wanted to know that in Dreiding energy, it does not calculate non

bonded forces or it deos? for example for a molecule of two atoms which

are not connected together, a complete force field model should

calculate the non bonded energy.

Current Dreiding implementation is developed to support 3D structure generation. It calculates only van der Waals energy for non bonded atoms. No charges or H-bonds are considered currently.

3D coordinate generation works on single disconnected molecular fragments. To maintain consistency energy calculation invoked on multi-fragment structures sums the energies calculated for the individual fragments.

So currently energy calculation works on single fragments; inside it only vdw considered. We are working on the implementation of MMFF94; as far as i know it will provide wider support of intermolecular interactions.

Regards,

Gabor

I am using molecule.getProperty("Energy") to get

the energy of the molecule. But for non bonded atoms it results zeroy.

I wanted to know that in Dreiding energy, it does not calculate non

bonded forces or it deos? for example for a molecule of two atoms which

are not connected together, a complete force field model should

calculate the non bonded energy.

oh, It's not good. It means that its energy calculation is not based on any of standars of Force field models yet, if I understand it well? Because I was going to implement this library because of its energy calculation. I wanted a complete force field like: "energy of non bondeds + energy of bondeds" which

energy of bondeds = E of dihedrals + E of angles + E of bond

So this library's energy calcualtion is not based on this fromula yes?

anyway, thanks

Hi,

It means that its energy calculation is not based on any of standars of Force field models yet, if I understand it well?

Sorry for the misunderstanding. The energy calculation is based on the Dreiding force field, which can be considered a standard MM approach.

I wanted a complete force field like: "energy of non bondeds + energy of bondeds"

Yes, energy is calculated this way. In our implementation "energy of non bondeds" contains only van der Waals energy components for non bonded atom pairs in the input structure.

Energy of bondeds = E of dihedrals + E of angles + E of bond

That's correct. In addition there is an inversion energy term additionally.

So this library's energy calcualtion is not based on this fromula yes?

So the calculations are based on the given formulae (with including inversion into E_bonded).

When the energy calculation is invoked on a Molecule which contains multiple disconnected fragments then the calculations are invoked on each fragment and the results are summed.

Could you tell us more details about your application and currently planned approach?

Regards,

Gabor

It means that its energy calculation is not based on any of standars of Force field models yet, if I understand it well?

I wanted a complete force field like: "energy of non bondeds + energy of bondeds"

Energy of bondeds = E of dihedrals + E of angles + E of bond

So this library's energy calcualtion is not based on this fromula yes?

Oh cool,

well actually we are working on the nanostructures optimization by soft computing methods.

Now I understand what you mean. But now I will face a problem when my molecule has only two atoms which are not bonded. Is there any other methods to calculate the energy between two non bonded atoms? I want the number of atoms of the molecule grows little by little and each time calculate the energy of the molecule. even if non bonded is added to it.

your great support is appreciated :)

Hi,

Thanks for the details.

Is there any other methods to calculate the energy between two non bonded atoms?

Currently it is not possible to call the force field this way.

Regards,

Gabor