[Open Babel] Can be listed in the Related projects List

I would like to introduce an algorithm MolBridge, *A program for finding non-bonded interactions in small molecule and biomolecule structures.* It uses Open Babel internally for finding the symmetry and aromatic rings. The homepage of MolBridge is: http://nucleix.mbu.iisc.ernet.in/molbridge/index.

Re: [Open Babel] How to assign numbers to H atoms name when converting PDB to MOL2 file?

My Idea: May be not direct but may work :) PDB files generally does not have Hydrogen atoms. In such case u can use 'REDUCE ' program from RICHARDSON Lab. Convert it to MOL2 format using Openbabel, which retains the atom nomenclature(This is the case only for PDB to MOL2, in all othercase, it give

[Open Babel] overlapping atoms of two molecules

Dear All I have two molecules with different atom labels.Is there any way of getting the overlapping atoms from both the molecules.. Thanking you in advance PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success ---

[Open Babel] Problem with the nomenclature of the atoms of the molecule

Dear All I have a cif file containing two molecules. When I convert the cif file to the PDB file, the ATOM NAME seems to be ATOM TYPE. Though it is in the same order as it was in cif, yet there is any method for getting the ATOM NAME not the TYPE (cif file has ATOM NAME). I becomes even more prob

Re: [Open Babel] --fillUC keepconnect option

l. > > Can't help more, sorry. > > Regards, > Pascal > > > >> babel -i cif PIZFAF.cif -o pdb a.pdb --fillUC keepconnect >> OpenBabel version is 2.2.3 (The latest version is not giving the proper >> results according to me and hence I am sticking to

Re: [Open Babel] --fillUC keepconnect option

PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success On Wed, Dec 19, 2012 at 3:43 PM, Pascal Muller wrote: > Hi, > > Seems that the .cif file is not attached. > Which command are you using exactly? > > Regards, > Pascal > > > 2012/12/19 pra

[Open Babel] --fillUC keepconnect option

I am using the --fillUC option with keepconnect for generating the symmetry mates. As per my understanding goes, by using this option, we should get full molecule. for example if the benzene molecule is having 12 atoms, so after generating the file using --fillUC option the number of atoms in the f

Re: [Open Babel] Atom type from Molreport option

Thanx alot for the reply. It was a great help to me. Prasun PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success On Tue, Dec 18, 2012 at 11:02 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > the atom type should be 'Car' as it is for Benzene molecule. >

Re: [Open Babel] Atom type from Molreport option

Sorry for not specifying exactly what I want. the atom type should be 'Car' as it is for Benzene molecule. thanx alot PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success On Tue, Dec 18, 2012 at 2:10 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > AN

[Open Babel] Atom type from Molreport option

Dear all I have a small molecule named ANULENE (File attached in the cif format). I am trying to generate the molreport which gives the information about the atom type of the molecule with other many informations. ANULENE is an aromatic molecule. To my surprise OpenBabel is giving C2 atom type to

[Open Babel] differences in the two versions of openbabel while using --fillUC

Hi all I was using OPENBABEL v 2.2.3 and now I have switched to v 2.3.1 I ran openbabel fo generating symmetry for BENZENE.cif and got two different files. I am attaching the files I think v2.2.3 was better for this option. Please have a look on the files and suggest me where I am going wrong I am

[Open Babel] Regarding symmetry problem

Hi all I am using OpenBabel for generating symmetry mates for BERZON.cif (file attached). It is having C 2m symmetry. I should get 8 equivalent points, but getting only 5. Can some body please help me. If possible can any one suggest me any other command line software that I can use. Regards PRAS

[Open Babel] lattice from unit cell

Dear all I have a small doubt regarding lattice preparation from unit cell of a molecule. Is there any command in Openbabel, which can generate lattice (3X3) If I will give the pdb file with CRYST1 record. I know fillUC can give unit cell. thanx in advance PRASUN (ASHOKA) Desire + stability = Res

[Open Babel] InChi notation of a small molecule

Dear all I am using Openbabel for converting pdb file to its corresponding inchi notation. Its working well, but problem is coming in identifying the real number of the atoms in the pdb files as Inchi notation is gives its own identifying number. Can some body help me in getting this information. T