I have derived the partial charges for a zinc ion in a catalytic site of an enzyme using R.E.S.P for the Amberffsb force field. For two of the three transition metals (the third belong to the non-catalytic domain so partial charges besides my own remain unknown) I have values from literature. Using PyRED I can derive the same partial charge values. All good so far.
Is there a clear step-by-step guide on how I take my new partial charges from R.E.S.P and add them to the amberffsb forcefield in the Gromacs forcefield file layout?
I have previously used the Gromos53a6 force field and I know that they deal with specific charge groups, unlike Amber which treats single atoms as a charge group in its own right (I could be wrong).
Thakns
It's rather simple. Likely you'll have a couple of ligating residues with noncanonical charges because of the coordinated metal ion, so you just need custom residues for each affected species (including the metal itself). Just follow:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Hi Justin, thanks again for the link earlier. I went through each step with the manual at hand and an example of a zinc finger using Amber FF in Gromacs 4.6.3. It all seems to make perfect sense and doesn't seem so difficult.
My only doubt though are the R.E.S.P partial charges from the literature that I have. I have reproduced the crystallographic R.E.S.P charges using their modified model i.e., they truncated the side chain with CH3 to avoid having a whole backbone. They used Amber along with the Amber10 FF. Given a truncated model I don't know how the partial charges in the new residue type would balance out. I am thinking that I would need to redo the R.E.S.P calculations using a whole residue. The literature was very vague how their derived charges were put into their FF.
Thanks
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