Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap

From: (wrong string) 曾晓� <deathsnake1991.gmail.com>
Date: Wed, 19 Dec 2012 18:20:33 +0800

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 - 02:30:03 PST