AMBER Archive (2009)

Subject: Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.

From: todd_at_semichem.com
Date: Sat May 09 2009 - 13:36:17 CDT

Dear Adrian,

Thanks for your answer!

But I think the question is still there even with these later force fields.

Also, I think the ff99SB still uses the 94 charges.

Todd

On Sat, 09 May 2009 14:07:08 -0400, Adrian Roitberg <roitberg_at_qtp.ufl.edu>
wrote:
> Dear Todd,
> I am sure more people will tel you this, but please, please please do
> not use Amber 94 parameters !
> They are not recomended anymore, and we have better stuff out there.
>
> Try instead ff99SB or ff03.
>
> Adrian
>
>
> todd_at_semichem.com wrote:
>> Hello,
>>
>> I am writing some code to assign AMBER 94 charges to proteins.
>>
>> I am using the data in the amino94.in, aminoct94.in and aminont94. files
>> from the amber10.ffparms download.
>>
>> These files contain 3 sets of charge data for LYS: non-terminal residue
>> form, amino-terminal (NH3+ end group) residue form and carboxyl-terminal
>> (COO- end group) residue form).
>>
>> However, only data for the non-terminal residue form of LYN (the
>> deprotonated form of Lysine, where the R group is neutral) appears to be
>> present.
>>
>> Aplogies if this data exists and I'm not finding it. But if not, what
is
>> the recommended procedure to deal with charges for terminal LYN
residues?
>>
>> Similarly, data for the terminal forms of GLH, ASH and CYM appears to be
>> absent.
>>
>> Lastly, does charge data exist for the neutral end group forms of the
>> amino-terminal and carboxy-terminal residues?
>>
>> Thanks!
>>
>> Todd
>>
>>
>>
>>
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>>

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