The problem with the structures in your images isn't the force field,
though you should certainly consider all options until you find the
one that is best for you.
The problem is that the residues were in the opposite order, so leap
didn't know how to bond them. Try the attached pdb. After loading,
use "bond m.1.C1 m.8.O4" (substituting for m whatever you named the
molecule).
If you ever don't feel like rearranging your pdb, as I've done here,
you can put TER cards between each residue and then bond them all
explicitly.
On Wed, Dec 19, 2012 at 11:10 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Dec 19 2012 - 11:30:03 PST
