AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 24 2008 - 07:49:03 CDT

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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