Hi,
I use xleap to build a PCA residue in my protein tail. When I try to load my molecule to xleap after assigning the force field parameters, I find that the program did not add the hydrogen atoms to the protein. This did not make any problem with tleap, where the hydrogens are properly added to the protein structure. I tried to use the edit graphical window and use the Add hydrogen & build optio in xleapn. The structure seems to have wrong valence assignment. Xleap seems to add the hydrogen atoms without considering the connection between the in the amino acid. in other word I've obtained an ensemble of atoms without any connectivity between them.
Have you any idea about this problem?
best regards
Houcemeddine Othman
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 29 2012 - 04:30:02 PDT
