Ranajit,
in the parameter file gaff2.dat - I assume that you used that one - the
respective comment says for hx:
"H bonded to C next to positively charged group"
(cf $AMBERHOME/amber22_src/dat/leap/parm/gaff2.dat)
And there are parameters for hx-containing bonds etc in the parameter file.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 26.07.2022 um 03:41 schrieb Ranajit Saha via AMBER:
> Hello All,
>
> I am generating a forcefield for n-butylammonium cation. I noticed (in
> the .ac file) that protons bonded to an sp3 carbon bonded to the
> positively charged N have atom type hx.
>
> ATOM 1 N1 nbu 1 -0.086 -0.084 -0.067 0.260958
> n4
> ATOM 2 C1 nbu 1 -0.887 1.122 -0.504 -0.182035
> c3
> ATOM 3 H1 nbu 1 -0.166 1.921 -0.652 0.115811
> hx <--
> ATOM 4 H2 nbu 1 -1.517 1.394 0.343 0.115811
> hx <--
> ATOM 5 C2 nbu 1 -1.729 0.938 -1.757 -0.136020
> c3
> ATOM 6 H3 nbu 1 -2.313 0.018 -1.701 0.071685
> hc
> ATOM 7 H4 nbu 1 -1.087 0.866 -2.637 0.071685
> hc
> ATOM 8 C3 nbu 1 -2.684 2.121 -1.934 0.148601
> c3
> ATOM 9 H5 nbu 1 -3.288 1.933 -2.822 0.008458
> hc
> ATOM 10 H6 nbu 1 -3.379 2.151 -1.091 0.008458
> hc
>
> I went through the literature and I did not see hx atom type in the
> amber atom type list (https://emleddin.github.io/comp-chem-website/AMBERguide-AMBER-atom-types.html).
>
>
> Is this atom type correct? Do I need to modify hx to hc in the .ac file
> manually and generate the force field?
>
> Please suggest.
> Regards
> Ranajit
>
>
>
>
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Received on Thu Aug 04 2022 - 13:37:27 PDT
