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: Sun May 10 2009 - 16:56:24 CDT

Dear Francois,

Thanks!

Todd

On Sun, 10 May 2009 07:49:55 +0200, FyD <fyd_at_q4md-forcefieldtools.org>
wrote:
> Dear Tod,
>
>> But I think the question is still there even with these later force
>> fields.
>> Also, I think the ff99SB still uses the 94 charges.
>
> Yes, you are right the charges comes from the Cornell et al. force
> field (ff94). The force fields that showed up after ff94 (i.e. ff96,
> ff98, ff99 or even ff99SB) derives all from the Cornell et al. force
> field. This is in ff94 that were designed the charges as you said, but
> also the force field atom types, the van der Waals parameters etc...
> Usually, these successive 'adapatations' (except for ff99) only
> contain several new dihedrals which were refited. Only the Duan et al.
> force field proposed a new set of charge values; using however the
> same rules for the force field atom type assignement.
>
>> 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.
>
> We have worked on Amber & GLYCAM force field conversion, and also used
> those *.in force field topology databases as reference for all the
> Amber force fields. See AmberFFC
> http://q4md-forcefieldtools.org/AmberFFC/
>
>> 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.
>
> You are right. Some fragments were not generated because not that
> often used I guess.
>
>> 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?
>
> You need to generate these "missing" (central) H2N-terminal and
> HOOC-terminal fragments. The reference in this type of work is:
> Cieplak et al. Application of the multimolecule and
> multiconformational RESP methodology to biopolymers: Charge derivation
> for DNA, RNA, and proteins. J. Comput. Chem. 1995, 16, 1357-1377.
> However, this reference only described the charged terminal residues...
>
> You can also look in R.E.DD.B. (closed until Monday) where you will
> find many different types of molecular fragments (you could follow as
> examples), and use R.E.D. or R.E.D. Server to generate your own
> fragments; See http://q4md-forcefieldtools.org/.
> You could also follow your own strategy, and by providing the required
> P2N input files for LYN, GLH, ASH and CYM you will generate what you
> need in a single R.E.D. job.
>
>> Similarly, data for the terminal forms of GLH, ASH and CYM appears to be
>> absent.
>
> Yes
>
>> Lastly, does charge data exist for the neutral end group forms of the
>> amino-terminal and carboxy-terminal residues?
>
> I do not know. You will find examples of such terminal fragments in
> R.E.DD.B.
>
> regards, Francois
>
>
>> 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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