Hi Francesco,
The DOT2 charges/radii don't look anything like AMBER charges (either
ff94-type or ff03-type) or radii to me. You can check this for
yourself if you have access to an AMBER distribution at the moment --
see $AMBERHOME/dat/leap/lib/all_amino94.lib (or all_amino03.lib) for
residue charges or $AMBERHOME/dat/leap/parm/parm99.dat for radii. As
a result, I would be very hesitant about incorporating AMBER
parameters into this program.
Maybe you would be better off taking a look at the charges/radii for
the Asn or Gln sidechains in DOT2, as these residues contain a
"terminal" -CONH2 group? At a minimum, the atomic radii would be
consistent that way.
Best,
Paul
On Aug 31, 2010, at 9:59 AM, Francesco Pietra wrote:
> 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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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Tue Aug 31 2010 - 11:00:03 PDT
