On Tue, Aug 31, 2010 at 6:40 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> Hi Francesco,
>
> By phenylalanine amide, do you mean a C-terminal (i.e., final residue
> of the protein/peptide) phenylalanine residue with a -CONH2 terminus
> instead of -COO(-)? If yes, then you just need to use the NHE residue
> in leap...
Yes, -CONH2 terminus. However, I am not using Amber itself now, rather
DOT2 (a protein-protein docking software from the S Diego
Supercomputer Center, which uses amber-type charges). I need to define
charges and radii for phenylalanine amide alongside default ones for
standard amino acids in a data file. For example for phenylalanine in
the various positions in a protein:
resi atom chrg epsi sigm radi end
PHE N -0.520 0.100 3.029 1.515
PHE H 0.248 0.020 1.782 0.891
PHE CA 0.214 0.000 3.296 1.648
PHE CB 0.038 0.100 3.421 1.711
PHE CG 0.011 0.100 3.296 1.648
PHE CD1 -0.011 0.000 3.296 1.648
PHE CE1 0.004 0.000 3.296 1.648
PHE CZ -0.003 0.000 3.296 1.648
PHE CE2 0.004 0.000 3.296 1.648
PHE CD2 -0.011 0.000 3.296 1.648
PHE C 0.526 0.100 3.296 1.648
PHE O -0.500 0.200 2.851 1.425
PHEC N -0.520 0.100 3.029 1.515
PHEC H 0.248 0.020 1.782 0.891
PHEC CA 0.208 0.000 3.296 1.648
PHEC CB 0.038 0.100 3.421 1.711
PHEC CG 0.011 0.100 3.296 1.648
PHEC CD1 -0.011 0.000 3.296 1.648
PHEC CE1 0.004 0.000 3.296 1.648
PHEC CZ -0.003 0.000 3.296 1.648
PHEC CE2 0.004 0.000 3.296 1.648
PHEC CD2 -0.011 0.000 3.296 1.648
PHEC C 0.444 0.100 3.296 1.648
PHEC O -0.706 0.200 2.851 1.425
PHEC OXT -0.706 0.200 2.851 1.425
PHEN N -0.263 0.100 3.029 1.515
PHEN H1 0.312 0.020 1.782 0.891
PHEN H2 0.312 0.020 1.782 0.891
PHEN H3 0.312 0.020 1.782 0.891
PHEN CA 0.269 0.000 3.296 1.648
PHEN CB 0.038 0.100 3.421 1.711
PHEN CG 0.011 0.100 3.296 1.648
PHEN CD1 -0.011 0.000 3.296 1.648
PHEN CE1 0.004 0.000 3.296 1.648
PHEN CZ -0.003 0.000 3.296 1.648
PHEN CE2 0.004 0.000 3.296 1.648
PHEN CD2 -0.011 0.000 3.296 1.648
PHEN C 0.526 0.100 3.296 1.648
PHEN O -0.500 0.200 2.851 1.425
Forget about epsi and sigm, not needed for my task.
francesco
>
> Best,
>
> Paul
>
>
> On Aug 31, 2010, at 9:31 AM, Francesco Pietra wrote:
>
>> Hello:
>> I am looking for Amber-type charges and radii for a modified residue:
>> phenylalanine amide (amidated phenylalanine). I have no suitable ab
>> initio software for using RED. Thanks for providing data or literature
>> reference. francesco pietra
>>
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>
>
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Received on Tue Aug 31 2010 - 10:00:05 PDT
