Hi,
PM6 method in amber can deal with so many elements:
PM6: H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu,
Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La,
Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi
Now I wanted to use amber to do QM/MM (PM6/GAFF) MD simulation. Antechamber is designed to be used with the GAFF, which covers almost all the organic chemical space that is made up of C, N, O, S, P, H, F, Cl, Br and I. For my studied system, there are some other elements, such as Boron (B) and silicon(Si), in my solute. In MD simulation£¬we use QM(PM6) to describe the solute region and MM(GAFF) to describe the solvent region. When I use Antechamber tools to generated amber inputfile, there will be some ' ATTN, need revision' cards in the solute frcmod files. I want to konw how can I generated correct inputfiles(.iprmtop and .inpcrd ) files automatically.
Thank you.
Best,
Manyi
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Received on Tue Nov 22 2016 - 17:30:03 PST
