[gmx-users] amber 03 forcefield

[shahab shariati]

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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