AMBER Archive (2009)

Subject: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?

From: quantum_mania_at_yahoo.com
Date: Fri Apr 17 2009 - 12:52:28 CDT

Hi Ross,

About the CG atom, what's happens if I load ff99SB before GLYCAM_06 in leap?

Thanks,

-DX

________________________________
From: Ross Walker <ross_at_rosswalker.co.uk>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Monday, April 13, 2009 9:10:38 PM
Subject: RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?

Hi Marek,

> In my opinion the ideal situation from the ff point of view could be to
> use for this complex system 3 forcefields
> in one time:
>
> ff99 or ff99SB - for oligonucleotides
> GAFF - for dendrimer residui
> GLYCAM_06 - for maltose
>
> Is it possible to load and use above mentioned forcefields in one time
> or

This should be possible. You can certainly load gaff with any of the above
force fields since it uses entirely lower case atom types and so does not
clash with any other force field. The only issue with mixing FF99SB and
GLYCAM_06 that I am aware of is with an atom type CG which is defined in
both force fields. However, I do not believe that FF99SB actually uses it
for anything so you have two options. Either 1. Edit parm99.dat and remove
all references to the CG atom or 2. make sure you always load GLYCAM_06
first.

Thus the simplest solution in your case would be to make sure you always
source things in the following order in Leap:

source leaprc.GLYCAM_06
source leaprc.ff99SB
source leaprc.gaff

Note the only remaining caveat here is that GLYCAM_06 uses SCEE and SCNB
scale factors of 1.0 while FF99SB and gaff use scale factors of 1.2 and 2.0
respectively. In AMBER 10 you cannot mix the scale factors, they are scalars
set for the entire simulation. I would recommend that you leave them at the
default of 1.2 and 2.0 since it has only a minor affect on the sugars. AMBER
11 will address this issue and allow mixing of 1-4 scale factors as a
function of 1-4 type.

Good luck,
Ross

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|\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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