Jarmila,
your analysis is correct. While ff03+bsc0 may be just fine (or may not, I
have not seen anyone check the balance of interactions with this mixed
charge model), I think that the physical rationale for ff99SB+bsc0 is a
little stronger. I have also used this combination in our protein-dna
simulations and have gotten excellent results.
On Mon, Nov 8, 2010 at 4:32 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jarmila,
>
>
>
> I saw your email from several days ago but have not had time to properly
> reply. You should post such questions to the amber mailing list since then
> you will get a more prompt reply and from people who can better comment on
> the appropriateness of certain force fields.
>
>
>
> My gut instinct would be to use FF99SB with BSC0 - we tend to see slightly
> better performance for proteins with FF99SB and the charge model is the
> same
> as that for BSC0 - I have not seen anything showing the compatibility of
> the
> point charge model between FF03 and other force fields that use a slightly
> different approach and so I am wary of this. I would suggest looking at
> what
> the authors used as the basis when they fitted BSC0 and go with this.
>
>
>
> Others might be able to comment more.
>
>
>
> As for Gromacs 4.5 with AMBER make sure you use double precision and NOT
> the
> pure single precision implementation as we have seen issues with this
> regarding energy conservation and stability.
>
>
>
> Good luck,
>
> Ross
>
>
>
> From: Jarmila Husby [mailto:jarmila.husby.gmail.com]
> Sent: Monday, November 08, 2010 2:38 AM
> To: rcw.sdsc.edu
> Subject: Amber force-field compatibility
>
>
>
> Dear professor Walker,
>
> I am about to set up an MD simulation of a large protein-DNA complex on
> Gromacs 4.5 (on Nvidia Tesla card) with Amber ports for gromacs. I would
> like to ask you about the compatibility of the Amber FF03 (for proteins)
> with bsc0 (for NA) versus the FF99sb with bsc0.
>
> My main focus of the simulation is the protein-DNA interaction, so I am
> searching the most favorable force-field combination. Personally, I would
> rather combine the parm99sb with bsc0 as they are both derived from
> parm94/99 with corresponding concept of deriving the partial charges. But
> recently I came across a number of papers (by Ramsden & Kunkel) where they
> used the combination of FF03+bsc0. Would you recommend this FF combination
> despite the FF03 is polarized and bsc0 is the parm99 "derivative"? What is
> the rational of these two force-fields being used together? And would you
> expect significantly different results between the parm99sb+bsc0 and
> FF03+bsc0 simulations?
>
> I would greatly appreciate your comments and suggestion.
>
> Thank you in advance for your reply,
>
> Best regards
> Jarmila
>
>
>
> Jarmila Husby, PhD Candidate
>
> CRUK PPI Drug Discovery/ BMSG Group
>
> Department of Pharm & Biol Chemistry
>
> The School of Pharmacy, University of London
>
> email1: jarmila.husby.live.pharmacy.ac.uk
>
> email2: jarmila.husby.gmail.com
> tel: (44) 0207 753 5996
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 08 2010 - 14:30:04 PST
