Re: [AMBER] phenylalanine amide

From: Francesco Pietra <chiendarret.gmail.com>
Date: Tue, 31 Aug 2010 18:59:05 +0200

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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 31 2010 - 10:00:05 PDT
Custom Search