Re: [AMBER] sulfonamide parameters for correct geometry

From: Junmei Wang <junmwang.gmail.com>
Date: Mon, 3 Feb 2020 13:01:45 -0500

Hi Annachiara,

I also tested the model compound benzene sulfonamide. I first generated
RESP charges for the model compound, generated a mol2 file using
antechamber with "-at gaff2", then I ran parmchk2 to generate frcmod file
with "-s 2" flag. After minimization, I superposed the minimized geometry
to the ab initio one and the rmsd is 0.037 Angestrom. The ca-sy-n8
angle is 103.5
and 101.4 for the ab initio and gaff2 optimized geometries, respectively.
benzene_sulfonamide.ac : ab initio optimized
min_aligned.pdb: gaff2 optimized

If you can send me the geometry of your molecules, maybe I can figure out
what's going on.

All the best

Junmei

On Wed, Jan 29, 2020 at 7:32 AM Annachiara TINIVELLA <
annachiara.tinivella.unimore.it> wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Mon Feb 03 2020 - 10:30:02 PST
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