I need a 3D structure of molecule for molecular dynamics simulation. I don't have a good chemistry background. I want a software which can assign the bond length, bond angle etc. automatically. Finally I want the geometry of the molecule to be energy minimized such that it is suitable for molecular dynamics simulation. Is there any free software? Also where can I have the bond lengths and bond angles etc. of a molecule (such as piroxicam)?
You want to have as the output .pdb file and use it in MD. Does this mean that you already have force field for your molecule? If not, it's more difficult story.
On what are you going to do MD?
I don't have the force field (GROMOS96) for the molecule. I am going to generate it with ATB (http://compbio.biosci.uq.edu.au/atb/index.py) server. I will use the energy minimized .pdb structure as an input to this server. For MD I will use GROMACS.
In this case it's simple. Take some chemical builder with the possibility of minimization. For example Ascalaph or ArgusLab.
Hi, I am using Ubuntu Linux distribution. ArgusLab don't have any linux version. Currenly, Ascalaph runs only under Windows.
However, if you have the support for Windows programs under Linux, it can work. At least I know that for Ascalaph.
Avogadro provides extensions for GAMESS, Gaussian, MOLPRO, MOPAC, NW Chem, Q-Chem. You can generate the input files for all these celebrated software. Avogadro provides with the basic geometry optimization. Then you can refine it at any level of theory using the other softwares.
only for measuring the bond distance and bond angle you can use Gauss view 3D, or chem draw 3D. Chem draw 3D will nicely energy minimize the structure with high efficiency, even it has a Guassian interface to choose the basis set you want for minimization. But these are not free.
For free version Avogadro, or MOPAC may work though MOPAC has a total number of atom limitation which is probably 1000.
You can use Avogadro as well as Chimera for minimization of the molecules. Both are installable and works fine in Ubuntu. If you want 3D minimized structure of small molecule (as it is not mentioned whether minimization required for which molecule-protein or small molecule), you may also use Gabedit software. Just install it from package manager in Ubuntu. You can also install spdb viewer using wine in Ubuntu and can also minimize the molecule using this software.
Best Regards,
Avogadro, Chimera, Gaussview, ChemDraw...there is a bunch of very intuitive programs designed to it .
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