Dear AMBER users,
I am currently using AMBER18 to run some MD simulations on a protein-ligand
complex. The ligand contains an undissociated benzene sulfonamide group
that is not coordinated to any metal atom.
As other users, I noticed that the sulfonamide group appears to have a
weird geometry, with the NH2 group forming almost a 90 degrees angle.
Moreover, as the simulation progresses the SO2 moiety appears to become
almost planar.
I tried to use either gaff or gaff2 parameters, but in both cases I
obtained the same results (the new N8 atom type by gaff2 is reported as
analogue to gaff N3)
The output in the generated frcmod using gaff2 (regarding the
sulfonamide atoms) is as follows:
ANGLE
ca-sy-n8 64.000 102.440 same as ca-sy-n3, penalty score= 0.0
hn-n8-sy 44.200 109.500 same as hn-n3-sy, penalty score= 0.0
n8-sy-o 70.400 107.130 same as n3-sy-o , penalty score= 0.0
hn-n8-hn 41.400 106.400 same as hn-n3-hn, penalty score= 0.0
DIHE
hn-n8-sy-ca 6 18.800 0.000 2.000 same as X
-n3-sy-X , penalty score= 0.0
hn-n8-sy-o 6 18.800 0.000 2.000 same as X
-n3-sy-X , penalty score= 0.0
IMPROPER
ca-ca-ca-sy 1.1 180.0 2.0 Using the
default value
NONBON
n8 1.8240 0.1700 same as n3
I tried to browse the mailing list archive and literature,but I could not
find a straight answer. I saw this issues being mentioned in other
messages, but some of them point to out-of-service servers such as
Wolf2pack.
I would like to kindly ask for your help to find the correct way to deal
with this issue. Please, let me know in case you need any further
information or clarification.
Thank you in advance for your time and consideration.
Kind regards,
Annachiara Tinivella
PhD student, Doctorate School in Clinical and Experimental Medicine
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Received on Wed Jan 29 2020 - 05:00:02 PST
