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Roger,<br><br>
<blockquote type=cite class=cite cite>1) #define gd_3
180.000 7.11 2<br>
; -C-OA- (carboxyl)
4.0<br><br>
2) #define gd_14 0.000
3.77 3<br>
; -C,CHn, SI-NT,NL,OA (sugar) 3<br><br>
3) #define gd_8 0.000
2.09 2<br>
; O-CH1-CHn-O 0.5<br><br>
In example 1, is it safe to assume that C and OA are the ith (first) and
lth<br>
(fourth) atoms of the four atoms that make up the dihedral angle.
If so,</blockquote><br>
I think that you will find that it actually means in 1) that it is a
dihedral defined around the 2 and 3 atoms of the dihedral, C and OA
respectively. So it is a chain of X-C-OA-Y and the dihedral is
around the central bond. Which makes sense since it is the nature
of the atoms on either side of the bond that generally dictate how the
dihedral around the bond will behave. When there are special cases
where the 1 or 4 atom also influence it, well that is shown in
3).<br><br>
<blockquote type=cite class=cite cite>would example 2 be describing a
system in which one could have a combination<br>
of C with NT, NL, or OA; or a combination of CHn with NT, NL, or OA; or
a<br>
combination of SI with NT, NL, or OA. Does the last example
(example 3)</blockquote><br>
2) to me means C-NT, C-NL, C-OA, CHn-NT ... etc. "-"
indicates a bond, "," separates the options/possible atoms that
it is applicable to.<br><br>
<blockquote type=cite class=cite cite>describe a system in which all four
atoms of the dihedral are being<br>
described in that particular order? Is this a special case where
all atoms<br>
are listed? Also, in all cases there is a number on the comment
line after</blockquote><br>
3) is a dihedral around a CH1-CHn bond, but there happens to be a O on
either end. So if there happens to also be a general CH1-CHn or
some variation somewhere else defined, but you have O-CH1-CHn-O in your
molecule, then use 3) instead as it is a special case.<br><br>
<blockquote type=cite class=cite cite>the atom types: Example 1 -
4.0, Example 2 - 3, and Example 3 - 0.5. What<br>
do these numbers represent?</blockquote><br>
No idea, haven't been able to work that one out. It is a comment
only and may come from GROMOS as a note or something?<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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