Re: [AMBER] ATP and Mg2+ parameters

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Tue, 8 Jul 2014 14:54:33 +0000

Hi All

Thank you for your suggestions.

On http://www.pharmacy.manchester.ac.uk/bryce/amber/ i found parameters for Mg2+.

Mg2+ frcmod:

Mg2+ vdw parameters from Magnesium Optimization Paper
MASS
MG 24.305 0.120 magnesium

NONB
  MG 1.5545 0.00295 Allner et al. JCTC , 8, 1493-1502, (2012)


For ATP I found the following frcmod parameters file:

# Modifications to the AMBER94 force field for polyphosphates
MASS
CT 12.01
OS 16.00
P 30.97
H1 1.008
O2 16.00
O3 16.00

BOND
CT-H1 340.000 1.090 from amber98
CT-OS 320.000 1.410
OS-P 230.000 1.61000
O2-P 525.000 1.480
O3-P 525.000 1.480 by analogy to O2

ANGLE
H1-CT-OS 50.000 109.500
H1-CT-H1 35.000 109.500
CT-OS-P 100.000 120.500
O2-P -O2 140.000 119.900
O3-P -O3 140.000 119.90 by analogy to O2
OS-P -O2 100.000 108.230
OS-P -O3 100.000 108.23 by analogy to O2
OS-P -OS 45.000 102.600
P -OS-P 12.685 150.000 J Comp Chem 2003, 24, 1016-1025

DIHE
H1-CT-OS-P 3 0.105 000.000 3.000 J Comp Chem 2003, 24, 1016-1025
O2-P -OS-CT 2 1.179 000.000 -3.000 J Comp Chem 2003, 24, 1016-1025
O2-P -OS-CT 2 -0.812 000.000 2.000 J Comp Chem 2003, 24, 1016-1025
CT-OS-P -OS 1 -1.560 0.0 1.0 J Comp Chem 2003, 24, 1016-1025
O2-P -OS-P 2 -0.709 0.0 2.0 J Comp Chem 2003, 24, 1016-1025
O3-P -OS-P 3 -0.255 0.0 3.0 J Comp Chem 2003, 24, 1016-1025
P -OS-P -OS 1 0.897 0.00 1.0 J Comp Chem 2003, 24, 1016-1025

NONBON
  H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
  O2 1.6612 0.2100 OPLS
  O3 1.6612 0.2100 OPLS - by analogy to O2
  CT 1.9080 0.1094 Spellmeyer
  P 2.1000 0.2000 JCC,7,(1986),230;
  OS 1.6837 0.1700 OPLS ether


It looks like parameters file only for the phosphates and not for the whole ATP.
How can I use it?

Best,
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |

Phone: +41 61 267 15 80


________________________________________
From: Alessandro Contini [alessandro.contini.unimi.it]
Sent: Tuesday, July 08, 2014 12:50 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ATP and Mg2+ parameters

Hi Valentina,
check in the amber parameters database

http://www.pharmacy.manchester.ac.uk/bryce/amber/

Updated parameters for divalent ions are also present in the
AmberTools14 distribution, accordingly to JCTC 2013, 9, 2733-2748 and
JCTC 2014, 10, 289-297

Hope this help.

Best regards

Alessandro

Il 08/07/2014 12:41, Valentina Romano ha scritto:
> Dear Amber users
>
> I would like to run a MD for a protein kinase in complex with ATP and a Mg2+ ion.
>
> Do you know if parameters for ATP and Mg2+ already exist?
> Or should I use antechamber?
>
> Thank you.
>
> Best,
> valentina
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
ResearcherID: F-5064-2012
URL: http://www.researcherid.com/rid/F-5064-2012
skype alessandrocontini
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Received on Tue Jul 08 2014 - 08:00:02 PDT
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