Dear deathsnake1991,
Sorry I did not read your previous emails. I just saw your email about
cyclodextrin.
You might be interested by the following paper:
http://www.ncbi.nlm.nih.gov/pubmed/21792425
& the following force field:
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
For cyclodextrins you can see that Glycam 2006 is not the best choice...
regards, Francois
> Dear Lachele Foley:
>
> Thank you for your email. It is very useful to me. ****
>
> However, I meet some new problems. I downloaded the pdb named *2ZYK, *which
> contains four gama-cyclodextrins and the water box. I ignore the other
> molecular expect one cyclodextrin. Then I modify the residue name in the
> pdb from *GLC* to* 4GA* so the pdb can be loaded in Leap successful and
> named as *A*. ****
>
> To my surprise, the molecular show a wrong structure(shown in* Fig.a*). As
> an attempt, I break all the 1,4-glycosidic bonds by typing *deletebond
> A.901.21 A.902.1* and so on. The result of this showed in* Fig.b*. After
> rebuild the 1,4-glycosidic bonds by typing *bond A.902.21 A.901.1*, I can
> nearly get what the structure I want(*Fig.c*). However , when observing the
> A.pdb gained by *savepdb A A.pdb*, I find the all the 1,4-glycosidic bonds
> are breaked again, just like the *Fig.b*. ****
>
> I get the *prmtop* and* inpcrd* file from variable *A* and use them to
> create the B.pdb by *ambpdb*. This pdb performs the same mistake with the
> initial pdb(*Fig.a*).****
>
> I feel crazy. Could you tell me what?s wrong with these?****
>
> Thanks for your help again. ****
>
> Best wishes for you.
>
> Fig.a
>
> Fig .b
> Fig.c
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Received on Wed Dec 19 2012 - 08:30:02 PST
