On Mon, Feb 20, 2012, pancham lal gupta wrote:
>
> In histidine (HIP) which is protonated at both sites,both nitrogen have NA
> atom type,in PARM 99 "NA" is defined for SP2 carbon
> but in both nitrogen one is +vely charged and SP3 hybridised. What should i
> interpret from this?
> NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS)
I'm not sure I understand your objection. The atom types in the HIP residue
look correct to me. The hybridization is never used for anything, and is just
descriptive. Still, neither of the nitrogens in HIP have sp3 hybridization.
>
> and ATOM TYPE for "TYM" and "ARN" are missing I haven't found in
> all_amino94.lib
I'm not sure what these residues are supposed to be; you are correct in
stating that they don't exist in all_amino94.lib (or in any other Amber
library, as far as I can see.)
...dac
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Received on Mon Feb 20 2012 - 06:00:02 PST
