AMBER Archive (2009)

Subject: [AMBER] force-field for cyclic oligosaccharide using leap

From: Madhurima Jana (tinni.217_at_gmail.com)
Date: Sun Jan 11 2009 - 22:21:23 CST

Hi All,

 I want to perform a MD simulation of beta-cyclodextrin molecule. For
 the system setup and force field I'm using Glycam06. The initial
 coordinates of the molecule are known to me. The residue named 4GB
 from GLYCAM_06.prep file I have chosen and create the force-field
 using leap programme from AMBER. But while loading the *.inpcrd file
 in vmd it is showing that there is no connecting bond between the
 sugar ring 7 & 1 means there is no connectivity between the O4 (ring7)
 & C1 (ring1). Whereas the other rings are connected properly. Also the
 *.prmtop file shows that there are total 153 bonds (NBONH+MBONA) which
 is expected to be 154. This also indicates there is the missing bond.

 Could anyone pls suggest me what is the wrong with me & how to overcome it.
 Any suggestion is highly accepted.

 Thanks in advance,

Madhurima

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