AMBER Archive (2009)

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

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Fri Apr 17 2009 - 13:13:49 CDT

I'm not Ross, but I know the answer. If you do it that way, leap
thinks your CG atoms should be sp2-type, meaning they only get three
bonds. This causes the bonding to be wacky in the topology file.
Atom positions might also be incorrect if using leap to assign
coordinates.

:-) Lachele

On Fri, Apr 17, 2009 at 1:52 PM, quantum_mania_at_yahoo.com
<quantum_mania_at_yahoo.com> wrote:
> 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
>
> /\
> \/
> |\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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber