On Tue, Jul 8, 2014 at 7:54 AM, Valentina Romano <valentina.romano.unibas.ch
> wrote:
> 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?
>
The rest of the parameters should already be present in the database.
Don't forget that adenine is a standard nucleobase that is present in most
simulations of nucleic acids. Those parameters have been around for quite
some time ;).
Also, I would suggest using the Mg2+ parameters recently developed in the
Merz group. They are available as a separate frcmod file depending on the
water model you plan to use. The Amber14 manual has a description of how
to use ions in your simulation: Chapter 3 section 6. There are 2 sets of
divalent ion parameters to choose from -- those that get the Metal-Oxygen
distance right and those that get the hydration free energy right (no sets
of parameters using the 12-6 LJ potential can get both). You'll have to
pick which one you want to use.
There is also a new 12-6-4 potential that performs better for divalent ions
you can try out as well (although it is significantly less-tested and
doesn't run on GPUs as of yet).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 08 2014 - 09:00:03 PDT
