Sir.......
"TYM" correspond to negatively charged tyrosine.
"ARN" correspond to neutral arginine.
they occur in protein when we increase the pH above 10.for neutral lysine
"LYN" atom type information
is there in amino_lib. but for negatively charged tyrosine "TYM" and
neutral arginine "ARN" atom type information
is not there.
what should i do?
should i proceed without these atom type information or can i create them?
pancham
On Mon, Feb 20, 2012 at 7:06 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 09:30:02 PST
