AMBER Archive (2008)

Subject: Re: AMBER: Query about the charge of atoms in the parmtop file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 24 2008 - 08:09:45 CDT

I would also think carefully about whether GLYCAM06 is compatible with ff03-
certainly they do not use the same charge model. You should be ok if you can
find papers that have validated the combination and show eg that Hbonds between
the 2 param sets are similar to those internally. Maybe not a major issue, but
it's kind of like mixing charmm and amber parameters together- who knows
what you will get? One should not assume. in my opinion, that all
"Amber" force
fields are the same and therefore can be mixed and matched. Keep a careful
eye on things like the charge model. My feeling is that simulations using
DNA, RNA, or other force fields using the 6-31G*/HF charge derivation procedure
should be kept with protein sets that do the same. I recommend ff99SB, but
with full disclore I have to say that I'm biased because that is from my lab.
However, the reason we made that force field was to have a good parameter
set that still had the same charge model as all of the non-protein
param sets that
people have developed over the years.
carlos

On Thu, Jul 24, 2008 at 8:49 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Madhurima,
>
>> I'm using leaprc.ff03 for protein and leaprc.GLYCAM_06 for the
>> carbohydrate. Now the selective part of the *.parmtop file generated
>> for my system is given below
>>
>> %FLAG CHARGE
>> %FORMAT(5E16.8)
>> 3.28183623E+00 3.50050383E+00 3.50050383E+00 3.50050383E+00
>> 6.70580640E-01
>>...
>> So the N terminal end of the protein is ASN. Now in "all_aminont03.in"
>> file it is given
>>...
>> So for terminal N atom of ASN (in parmtop file) charge =
>> 3.28183623E+00/18.2223 = 0.18009 which is not equal to the value of
>> -0.669106 given in the above table.
>
> Last time I tried out FF03 for some reason there were no terminal residues
> defined so all regular residues used the FF03 charges while the terminal
> residues used FF99 (FF94) style charges. This was a concous decision made as
> part of the FF03 development - I.e. they only refitted the charges on
> regular residues. Was this a valid decision, in my opinion probably not, but
> maybe there is evidence that it is perfectly okay, I would ask the FF03
> developers for their opinions on that.
>
> What you are seeing here is likely that behavior, I.e. the N charge here
> probably matches that of NASN from FF94. In fact if you take a look in the
> leaprc.ff03 leap file you will see exactly this:
>
> loadOff all_aminoct94.lib
> loadOff all_aminont94.lib
> loadOff all_amino03.lib
>
> So leap does exactly what is asked of it. All the C and N terminals use FF94
> charges while all the standard residues use FF03 charges.
>
> If you check the amber 10 cmd directory you will see there is also a
> leaprc.ff03.r1 file (which I just discovered myself). This does the
> following:
>
> loadOff all_aminoct03.lib
> loadOff all_aminont03.lib
> loadOff all_amino03.lib
>
> Which will then use the FF03 CT and NT charges. Interestingly a paragraph on
> this just appeared in the AMBER tools manual:
>
> "The original model used the old (ff94) charge scheme for N- and C-terminal
> amino acids.
> This was what was distributed with Amber 9, and can still be activated by
> using leaprc.ff03.
> More recently, new libraries for the terminal amino acids have been
> constructed, using the same
> charge scheme as for the rest of the force field. This newer version (which
> is recommended for
> all new simulations) is accessed by using leaprc.ff03.r1."
>
> I don't blame you for missing this - I just found it myself. But it looks
> like if you use the .r1 file you should get the charges you expect.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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