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Hi Mattia,
Thank you for the link below. I have a question. Do you know if i can study DNA strand(s) on Si or Au surfaces, are there forcefields that describe theses surfaces in AMBER.
Thank you for your help,
Taufik
Mattia Mori - CERM wrote:
In this paper you can find good Zinc parameters for Amber Force Field-----------------------------------------------------------------------
Tuccinardi T, Martinelli A, Nuti E, Carelli P, Balzano F, Uccello-Barretta
G, Murphy G, Rossello A.
/Bioorg. Med. Chem/. 2006 14(12),
4260-4276
Or you can download
http://www.mmvsl.farm.unipi.it/downloads/free-downloads/amber-ff-parameters-for-the-zinc-hydroxammate-interaction/
For Calcium ions you can find parameters in related papers or databases.
Regards
Mattia
Madjid Taghdir ha scritto:
Dear amber users,
Hi
I am trying to simulate a protein with two heteroatom (Ca and Zn) that cordinated to its structure. how can I find the force constants and equilibrum bond , angle and so on.
Best regards
Tghdir
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Mattia Mori, PhD Student
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-- **-**-**-**-**-**-**-**-**-**-**-**-** Mattia Mori, PhD Student CERM - Centro di Risonanze Magnetiche via L. Sacconi 6,, 50019 Sesto Fiorentino, FI fax (+39) 055 4573914 tel (+39) 055 4573912 www.cerm.unifi.it----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu Received on Sun Dec 09 2007 - 06:07:25 PST