You can either try to find the molecule in some small molecule database e.g. ZINC http://zinc.docking.org/

or build AND MINIMISE the 3D structure in some editor like open source AVOGADRO avogadro.openmolecules.net/

Take a look at Open Babel. It converts many different formats. http://openbabel.org/wiki/Main_Page

Open babel is the best converter of molecular formats. If in case you need to convert 2d to 3d then either use an on-line format converter or Accelry's discovery studio

if you have the PubChem ID of the molecule you want to use, you can find its 3D structure on the website in SDF file format and downloaded it.

if you want to change the format you can use openbabel or babel on linux computer with this following command line: babel -isdf molecule.sdf -opdb molecule.pdb

or directly open the sdf format file on every molecular viewer and use the viewer for convert.

as Jan Brezovsky says, avogadro is a good choice.

yes, Open babel is good for molecular format conversion

The simplest way to convert any molecule is openbabel. If you using Linux you can type in terminal: babel ?.pdb ?.mol2 (? stands for any name or pdb code) or babel *.pdb *.mol2 for all files in the directory. I think there is a Windows version too, but I have never used it.

You can use either OpenBabel (http://www.chemie.fu-berlin.de/chemnet/use/babel.html) or PRODRG2 (http://davapc1.bioch.dundee.ac.uk/prodrg/index.html). You can also explore ACPYE (http://code.google.com/p/acpype/w/list) or HIC-UP. I would prefer first two!

several programs can to convert to different formats. In this moment, I am using Maestro software (Schrödinger), because I am using several programs that are connected by this interface (It's free for academic users). This program is for Windows, Linux or Mac.

Do what sergio has suggested above.

Maestro program can to change format file of the structures

i have mac OS, so have to try with which tool or software i can do, thanks all ...

U can Use Chimera as well.

I agree with Sergio Aguila, Maestro is a very good program and Open Babel, cited by Neeraj Misra, is so good too.

if you knew PyMol, you can use it for converter. just open your molecule and save molecule in other format. it's so simple...

the best way is to copy the SMILES format pertaining to PubChem ID. Put it in Chemsketch, Marvin Sketch, etc and generate 2D and optimize into 3D which eventually will help you to understand the optimized molecules and its 3D structure. Since you have not provided the query with it is a 2D or 3D SDF.

If you know the stucture of the molecule you can draw it in chemsketch and you can save it in mol format then you can convert it into pdb file format using online smiles convertor[ you require smiles notation which can be generated using chemsketch]

Use Babel. This is the most straight forward file format converter. Pawan gave you the link.

http://www.vcclab.org/lab/babel/

You can use babel program to convert the file in any format.

thanks all for helping me, I got my answer....

I can recognize that you are using AutoDock for docking purpose. Better, use PyRx, A easy interface to convert any file formats (embedded with Open Babel). Unsurprisingly, you can minimize your structure by classical or all atom force fields. Since this program is engineered to perform Virtual Screening with the implementation of ADT as background, you may face no problem in using this software.

Hello!

I'm trying to convert a batch of molecules SDF to mol2 with open babel, but I get this message:

babel: cannot read input format

What happens?

I have used UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) to save either PDF or Mol2 files of small molecules. Use "Tools-> Structure Editing-AddH" to add hydrogens.

Molecule file conversion with MolConverter

MolConverter is a command line program in Marvin Beans and JChem that converts between various file types.

Check following link

https://chemaxon.com/marvin-archive/3.3.3/marvin/doc/user/molconvert.html

use open babel http://openbabel.org/wiki/Main_Page

You can use Babel converter.

Good Luck

http://pasilla.health.unm.edu/tomcat/biocomp/convert

use pymol software

you can get the smiles notation of the structure from pubchem database then using the online software online SMILES translator to convert it into the PDB file format