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<div>If you back the origional papers alot of the conversions can be found. I dont know the papers off the top of my head,</div>
<div>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...</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 25. März 2013 um 16:56 Uhr<br/>
<b>Von:</b> "Anna MARABOTTI" <amarabotti@unisa.it><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] Re: Re: help with chromophore of a GFP</div>
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<br/>
Dear gmx-users,<br/>
<br/>
I'm still dealing with my problem of obtaining<br/>
parameters for my chromophore of the GFP family, in order to treat it as<br/>
a new residue. I'm trying (VERY hardly) to add missing parameters into<br/>
ffbonded.itp file for AMBER99SB ff, using those parameters found in<br/>
files calculated by Antechamber. To date, I've added those parameters<br/>
related to bonds, now I have to add those related to angles, dihedrals<br/>
and impropers.<br/>
<br/>
I'm dealing with section [angletypes] of file<br/>
ffbonded.itp, and I'm looking at the values of cth (that I imagine is<br/>
the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see<br/>
that all parameters in ffbonded.itp are multiple of the value of 4.184,<br/>
corresponding to the conversion factor between kcal and kJ. If I divide<br/>
each of these values, I obtain a value corresponding to a number such as<br/>
80, 70, 120, 40 etc. Instead, if I look at those corresponding values<br/>
found using Antechamber, I see, as expected, numbers with decimals, that<br/>
are often very different from those present in ffbonded.itp (when I<br/>
compare angles present in both files). For example, for the angle<br/>
CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72<br/>
kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of<br/>
63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which<br/>
is different from the value of Antechamber. If I consider the angle<br/>
CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is<br/>
46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184<br/>
is exactly 100.<br/>
<br/>
Moreover, the same values of angles and forces are<br/>
applied to angles that in my opinion are quite different among them. For<br/>
example, I found the same value of 109.5 (th) and 418.4 (cth) for:<br/>
H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1,<br/>
H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very<br/>
different to me, and I'd expect to find different values of these<br/>
parameters.<br/>
<br/>
It seems to me that values into ffbonded.itp related to<br/>
these force constants are quite "strange", especially for the fact that<br/>
they are EXACTLY multiple of 4.184, and I wonder if I'm correctly<br/>
interpreting these values.<br/>
<br/>
Best regards<br/>
<br/>
Anna<br/>
<br/>
--<br/>
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