???? 25/08/2018 05:10 ??, ?/? Tai Tze Hong ??????:
> Hi,
>
>
>
> I am working on an inclusion complex of (2-Hydroxypropyl)-?-cyclodextrin
> and a ligand. I added hydroxylpropyl group to the beta cyclodextrin
> structure, which i get it from pdb.
>
>
>
> I have no idea of starting this. Can anybody guide me for getting the
> solvated complex of hydroxylpropylcyclodextrin-ligand in tleap? Here is my
> structure of HPCD.
>
>
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Hi Tai,
first of all GLYCAM (1) and q4md-CD (2) force fields should be used here.
The most tricky part is to create suitable .lib files for each glucose
unit (residue) of your cyclodextrin and for hydroxypropyl groups.
Gaussian or GAMESS can be used to assign charges for the hydroxypropyl
groups. Then use "bond" command to connect the 7 CD residues in the
structure.
Thus, the final pdb file, should look like this (com.pdb).
1. K. N. Kirschner, A. B. Yongye, S. M. Tschampel, J. Gonzalez-
Outeirino, C. R. Daniels, B. L. Foley, and R. J. Woods, GLYCAM06:
A generalizable biomolecular force field, carbohydrates. J. Comput.
Chem. 29, 622 (2008).
2. C. Cezard, X. Trivelli, F. Aubry, F. Djedaini-Pilard, and F. Y.
Dupradeau, Molecular dynamics studies of native and substituted
cyclodextrins in different media: Charge derivation and force field
performances. Phys. Chem. Chem. Phys. 13, 15103 (2011).
You can see a recent publication from our lab:
https://doi.org/doi:10.1166/jbn.2017.2374
Hope that helps,
Elias
--
Elias D. Christoforides, PhD
Agricultural University of Athens,
Department of Biotechnology,
Physics Laboratory, Room 27-1
Iera Odos 75, 11855 Athens,
Greece
Tel: +302105294225
Fax: +302105294233
Email: el_chr.aua.gr
http://echristoforides.webnode.com//
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Received on Mon Aug 27 2018 - 07:00:02 PDT
