AMBER Archive (2009)
Subject: Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
Date: Sat May 09 2009 - 13:36:17 CDT
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.
On Sat, 09 May 2009 14:07:08 -0400, Adrian Roitberg <roitberg_at_qtp.ufl.edu>
> 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.
> todd_at_semichem.com wrote:
>> 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
>> Aplogies if this data exists and I'm not finding it. But if not, what
>> the recommended procedure to deal with charges for terminal LYN
>> Similarly, data for the terminal forms of GLH, ASH and CYM appears to be
>> Lastly, does charge data exist for the neutral end group forms of the
>> amino-terminal and carboxy-terminal residues?
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