shahab shariati wrote:
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?
AMBER03 was derived from AMBER99, with the principal changes being
reparameterization of charges, so the nonbonded atom types are unchanged.
Besides, atom types are just labels, you can call them anything you want, but in
essence, some parameters are identical between the two force fields.
-Justin
Any help will highly appreciated!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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