AMBER Archive (2009)

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

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Tue Apr 14 2009 - 18:18:18 CDT

Dear Ross,
thank you very much for your complex and valuable answer !

Just for the curiosity, is this discussed combination:

  GLYCAM_06 + ff99SB + GAFF

remarkably better solution than only:

ff99SB + GAFF

       ?

I mean if GAFF forcefield is able to parametrise maltose (I think it is),
it is still
worth to add also GLYCAM ff in my case (considering also that little
problem with different
scaling factors) ?

Best regards,

   Marek

Dne Tue, 14 Apr 2009 06:10:38 +0200 Ross Walker <ross_at_rosswalker.co.uk>
napsal/-a:

> 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 |
>
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