AMBER Archive (2007)

Subject: Re: AMBER: Zinc-Histidine force field

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Thu Nov 22 2007 - 13:12:43 CST

Thank you very much!!
I'll try to set torsional parameters to zero.
I'll update you about my progress in that way as soon as possible!
All the best

Mattia

Ray Luo ha scritto:
>
> Antechamber can translate your QM output file to prepin file. Atomic
> charges should be automatically fitted by a call to RESP within the
> program. But torsion terms are a lot harder to tune if you can’t find
> them. However, I’m not sure you have to worry about torsion terms if
> you are using a covalent zinc-binding interface. We were able to
> reproduce the vibration frequencies of the zinc interface with
> zinc-related torsion terms set to zero.
>
> All the best,
> Ray
>
> ==========================================
>
> Ray Luo, Ph.D.
>
> Dept Molecular Biology & Biochemistry
>
> University of California, Irvine, CA 92697
>
> USPS: PO Box 3900
>
> Phone: (949) 824-9528
>
> Email: rluo_at_uci.edu
>
> Web: http://rayl0.bio.uci.edu/
>
> ==========================================
>
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Mattia Mori - CERM
> *Sent:* Thursday, November 22, 2007 4:06 AM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: Zinc-Histidine force field
>
> thank you for the paper, I'm reading it. I'm running QM calculation on
> the zinc-histidine system to calculate the charge, but what I don't
> know is how to incorporate them in a new force fields and how to
> calculate torsional parameters? I'll get them in the gaussian ouyput?
> Should I modify manually the force field or is better to use
> antechamber to obtain the .prepi for the small system?
>
> Best,
>
> mattia
>
> Ray Luo ha scritto:
>
> You can borrow some parameters from our following study on the p53 DNA
> binding domain:
>
> Molecular Dynamics Simulations of p53 DNA-Binding Domain, Lu, Q.; Tan,
> Y.-H.; Luo, R., J. Phys. Chem. B., 2007, 111(39), 11538-11545.
>
> In general, you'll have to do some QM calculations to get the parameters for
> your specific system.
>
> Best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900
> Phone: (949) 824-9528
> Email: rluo_at_uci.edu <mailto:rluo_at_uci.edu>
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu <mailto:owner-amber_at_scripps.edu> [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Mattia Mori - CERM
> Sent: Wednesday, November 21, 2007 8:54 AM
> To: amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> Subject: AMBER: Zinc-Histidine force field
>
> Dear amber users,
> I'm trying to work with zinc protein but I got some problems during the
> parametrization with tleap.
> When I bound the Zn ion to the NE2 of the three histidins with the command
> "bond" and saveamberparm I get this error message:
>
> Could not find bond parameters for : NB - Zn
> Could not find angle parameters for: CV - NB - ZN
> Could not find angle parameters for: CR - NB - ZN
> ......
> parameter files was not saved
>
>
> I think I've to built the .prep file and/or to modify the force field for my
> protein but I don't know how to do that.
> Do someone can tell me if there are some tutorials about? or where to find a
> reliable forcefield fo MMPs protein?
>
> thank you very much.
>
> Mattia
>
>
>
>
>
>
>
>
> --
>
>
>
>
>
>
> **-**-**-**-**-**-**-**-**-**-**-**-**
>
> 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 <http://www.cerm.unifi.it>
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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

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