If you back the origional papers alot of the conversions can be found. I dont know the papers off the top of my head,
so you should just ask your PI, collegues or the board. They are a pain, one paper will have 2 and be missing one definition you want, etc...
Stephan Watkins
Gesendet: Montag, 25. März 2013 um 16:56 Uhr
Von: "Anna MARABOTTI" <amarabo...@unisa.it>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Re: Re: help with chromophore of a GFP
Von: "Anna MARABOTTI" <amarabo...@unisa.it>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Re: Re: help with chromophore of a GFP
Dear gmx-users,
I'm still dealing with my problem of obtaining
parameters for my chromophore of the GFP family, in order to treat it as
a new residue. I'm trying (VERY hardly) to add missing parameters into
ffbonded.itp file for AMBER99SB ff, using those parameters found in
files calculated by Antechamber. To date, I've added those parameters
related to bonds, now I have to add those related to angles, dihedrals
and impropers.
I'm dealing with section [angletypes] of file
ffbonded.itp, and I'm looking at the values of cth (that I imagine is
the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see
that all parameters in ffbonded.itp are multiple of the value of 4.184,
corresponding to the conversion factor between kcal and kJ. If I divide
each of these values, I obtain a value corresponding to a number such as
80, 70, 120, 40 etc. Instead, if I look at those corresponding values
found using Antechamber, I see, as expected, numbers with decimals, that
are often very different from those present in ffbonded.itp (when I
compare angles present in both files). For example, for the angle
CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72
kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of
63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which
is different from the value of Antechamber. If I consider the angle
CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is
46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184
is exactly 100.
Moreover, the same values of angles and forces are
applied to angles that in my opinion are quite different among them. For
example, I found the same value of 109.5 (th) and 418.4 (cth) for:
H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1,
H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very
different to me, and I'd expect to find different values of these
parameters.
It seems to me that values into ffbonded.itp related to
these force constants are quite "strange", especially for the fact that
they are EXACTLY multiple of 4.184, and I wonder if I'm correctly
interpreting these values.
Best regards
Anna
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