On 8/2/19 8:59 AM, Dawid das wrote:
Thank you for an asnwer. However, I still need to ask more.
So, let's take this time the
NR1 CPH1 CPH2 H
NR1 CPH2 CPH1 H
example. For such quartets, the improper dihedral parameters are defined
for HSD residue.
Now, the bonding is as follows in part of HSD:
H
|
NR1
/ \
CPH1 CPH2
In my top file generated with pdb2gmx I can see the improper dihedral
entries for both
NR1 CPH1 CPH2 H
NR1 CPH2 CPH1 H
Also after dumping the tpr file I can see IDIHS entries for both
arrangement of atoms for the same molecule.
According to Gromacs manual, the entry for improper dihedral i j k l is
understood as follows
l
|
i
/ \
j k
So maybe I'm blind but I still don't really understand the purpose of
changing the middle atom types
if there is in fact only one way these four atoms are connected in HSD. The
only reason I see is to
make it more rigid because I have "doubled" improper.
Again, I would not call it a "doubled" parameter, because they are
clearly different in atom order. This usually implies a difference in
stereochemistry; in this case, I don't know the history of why the
impropers are assigned this way, but going back to the original CHARMM
topologies there are in fact two impropers assigned around ND1, CD2, and
CE1. The use of two terms with the same parameters but different
connectivities is probably due to having to avoid some kind of
asymmetry, though it seems unusual. Regardless, it is a faithful (and
correct) representation of the force field and we have tested it for
agreement between CHARMM and GROMACS.
-Justin
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Justin A. Lemkul, Ph.D.
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