Hi gromacs users I will use amber 03 forcefield for simulation of protein-dna interaction. but why ffamber03.atp is as follow :
amber99_0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) amber99_1 79.90000 ; BR bromine amber99_2 12.01000 ; C sp2 C carbonyl group amber99_3 12.01000 ; CA sp2 C pure aromatic (benzene) amber99_4 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction amber99_5 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS amber99_6 12.01000 ; CK sp2 C 5 memb.ring in purines amber99_7 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 amber99_8 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) amber99_9 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N amber99_10 12.01000 ; CR sp2 arom as CQ but in HIS why amber99 instead of amber03? Any help will highly appreciated!
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