I'd like to run MD simulations of lectins in complex with glycans such as lactose using Gromacs. What is the best way to define the parameter and topology for lactose that are compatible with OPLS, amber, charm and/or gromos force fields with explicit water model?
I would advise you first to check if there is not some litterature for these parameters in the litterature.
Then, for charges, a good starting point could be the charges obtained from a quantum calculation (for instance with GAUSSIAN), preferably with a PCM corresponding to your medium
For bond, angles, diedrals, and LJ parameters, you should be able to find in the litterature the energy or using the parametrization of atoms (for instance codes CT HT in OPLS). The values for lenghts and angles could be taken from your structure file calculated previously for charges.
Hello,
You could have a look at the parameters provided in the latest Glycam distribution..they can safely be used with some version of the AMBER force field and it would save you the pain of parametrising them using QM approaches...have a look here: http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/
I have previously simulated some galacturonan moieties in combination with carbohydrate-binding enzymes successfully using it...
Hope this helps.
Cheers,
Davide
Thanks Davide - I'll have a look into it. Is this compatible with Gromacs? It is not obvious to be from the web link...
Hello Danny,
Definitely compatible..I used it with Gromacs. You could use Leaprc/Antechamber to retrieve the correct format that Gromacs uses.
Have a look at here: http://ambermd.org/tutorials/basic/tutorial4b/
This can also help: http://ambermd.org/doc6/html/AMBER-sh-5.8.html
Parameters and library/leaprc files in the AMBER format should be already provided on the Glycam webpage here:
http://glycam.org/docs/forcefield/parameters/
In the end it will be just a matter of following the tutorial (and skipping the steps you don't need..) in order to obtain the right format to run GROMACS.
Cheers,
Davide
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