Re: [AMBER] about amber force field

From: Alan <>
Date: Mon, 22 Mar 2010 13:59:35 +0000

Hi there,

I will do something similar but with ligands and so far I am strongly
considering ff99SB for everything.

BTW, ff99SB (2006) is newer than ff03 and ff03 wouldn't be "compatible" with
GAFF for example IMHO.

[ff99SB] Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and
Simmerling, C. Comparison of multiple amber force fields and development of
improved protein backbone parameters. *Proteins-Structure Function and
Bioinformatics 65*, 3 (NOV 15 2006), 712–725.

[ff03] Duan, Y., Wu, C., Chowdhury, S., Lee, M., Xiong, G., Zhang, W., Yang,
R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. A
point-charge force field for molecular mechanics simulations of proteins
based on condensed-phase quantum mechanical calculations. *Journal of
Computational Chemistry 24* (2003), 1999–2012.


On Mon, Mar 22, 2010 at 13:08, mattia <> wrote:

> Hi,
> For sure you have to minimize the protein structure (and the solvent, if
> present), before to attempt MD simulations.
> For a similar system (protein-DNA) I've succesfully used ff99SB for nucleic
> acids and ff03 for the protein, modified with Zn-binding parameters [Mori M
> et al., J Chem Inf Model. 2010 Mar 4. (Epub ahead of print)]. Just load both
> of them in leap module.
> About the version of Amber, I've used without problems AMBER10. I think
> the MMPBSA test problem has been already fixed, check the archive.
> However Amber9 should also works fine.
> Regards
> Mattia
> geyan ha scritto:
>> Hi all amber users,
>> I want to do MD about a system of proteins and DNA complex. Before the
>> MD,I think the first step is to minimize the protein 3D structure which is
>> produced by homology modelling.
>> My question is choosing which force field for protein,which one for
>> DNA, and which one for the complex?all using ff99SB?
>> By the way,amber9 and amber10,which one is better?I have heard of many
>> unexpected problems for amber10 and I met one in MM_PBSA test
>> --------------
>> geyan
>> 2010-03-22
>> _______________________________________________
>> AMBER mailing list
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> AMBER mailing list

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Mon Mar 22 2010 - 07:30:02 PDT
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