AMBER Archive (2004)

Subject: AMBER: averaged structure with unknown elements

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Wed Feb 25 2004 - 15:32:54 CST

Dear all AMBER users,

After averaging a structure from the MD trajectory in PDB format, I loaded
this structure into xleap to make top and crd files for energy
minimization. When I was loading pdb file into xlaep, I got a message "leap
added 2594 missing atoms according to residue templates: 2584 H/lone pairs,
10 unknown element". But I could save the prmtop and inpcrd files for this
structure without complaints. So I wonder what are the possible unknown
elements and if they affect the energy minimization?

Thanks in advance.


Youyi Peng

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