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I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.

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You have several options to generate smaller peptides using the peptide builders in

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  • $\begingroup$ Is that all or should I then get a more advanced software $\endgroup$ – SaudiBombsYemen May 5 '15 at 17:30
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    $\begingroup$ @PabloXd There are probably some commercial tools for the job, but the two I mentioned are open source, available at no cost, run under Linux, OSX and Windows and you can automate tasks using Python scripts. Btw, if you found my answer helpful on this site, I'd appreciate if you'd accept it. You can always unaccept it later if somebody else provides a better answer ;-) $\endgroup$ – Klaus-Dieter Warzecha May 5 '15 at 18:32
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The free component of the AMBER molecular dynamics package, AmberTools, contains a very nice interface (tleap) for automatically generating coordinates of peptides and proteins from a sequence of three-letter amino acid codes. There's a tutorial on how to build and simulate a peptide using AMBER, but you don't have to run the dynamics. You can use the peptide building functionality on its own. It exports a pretty standard PDB file once you're done.

You could write a Python script that generates the tleap input, or if the peptide is short enough, write a tleap script with the three-letter amino acid codes by hand.

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