Dear all,
I want to do a molecular dynamic simulation of Amino-acyl t-RNA synthatase enzyme with its substrate ATP, AMP and t-RNA. So please suggest me which force field is best for this type of simulation. I found in various articles they use Amber or Charmm force field. If amber then how i generate the ligand topology by using online server.
Please help me
Hi Rohit,
Normally, for standard molecules like proteins and nucleic acids, the topology parameters for amino acid and nucleic acids, respectively, must be in built in the force field. You should figure out how to give the sequence input to build the topology automatically. On the other hand, if you have the .pdb sequences of the input files, you may use babel scripts (should be available for free) to convert the .pdb files into the required Gromacs-ff format.
best regards,
Uday.
Thanks dear,
But i want to know. How i generate the ligand topology by using Amber force field
If you have the .pdb files of the structures (either from X-ray or NMR structures or you can simply construct the sequence on free software online), please use pdb2gmx tool with ff definition using -ff flag. (http://manual.gromacs.org/programs/gmx-pdb2gmx.html)
For generating the ligand topologies and parameters for AmberFF you can use Antechamber and then Acpype.
http://ambermd.org/tutorials/basic/tutorial4b/
https://code.google.com/p/acpype/
Just to add a further comment: Amber is rather a "family" of force fields.
For simulations with nucleic acids, I would suggest, specifically, amber parmbsc0.
Regards
Paulo Netz
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