Hello Paul:
The program has a complex turnaround, initially needing partial atomic
charges for amino acid residues with polar hydrogen atoms only (Weiner
et al., (1984), J. Amer. Chem. Soc. 106, 765-784) (i.e, Amber). The
library uses the format of University of Houston, Brownian Dynamics
program (Gilson et al., (1993) J. Phys. Chem. 97, 3591, from which
epsi and sigm). I forgot to mention that I need those old-fashioned
Amber charges and radii, in fact I was probably wrong in mentioning
RED to this concern.
francesco
On Tue, Aug 31, 2010 at 7:34 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> 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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>>>
>>>
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Received on Tue Aug 31 2010 - 14:30:03 PDT
