[gmx-users] amber 03 forcefield

[Justin A. Lemkul]

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!
> 

-- 
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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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