AMBER Archive (2004)

Subject: AMBER: Defining residues

Date: Sat Feb 21 2004 - 22:34:56 CST

('binary' encoding is not supported, stored as-is) Dear Amber community,

I am working with a molecule with AB2 connectivity. Therefore I defined
the residue in question, with 1 head group (the A side) and 2 tail groups
(the B side). Now when I read in the molecules pdb file, naturally after
reading in the *.lib files, I get the following error:

One sided connection. Residue: missing connect1 atom. (60 times)
   total atoms in file: 1092
   Leap added 60 missing atoms according to residue templates:
     60 H / lone pairs

There are 61 residues. The center residue, which has 4 B groups,
therefore 4 tail defintions, seems to be ok. What does this error mean?
How do I address it?
I followed the instructions given on the amber website on how to define a
The specific commands I used to set the head and tail groups are as follows:
 set RES head RES.1.H1
 set RES tail RES.1.H11
 set RES tail RES.1.H12
 set RES.1 connect0 RES.1.H1
 set RES.1 connect1 RES.1.H11
 set RES.1 connect1 RES.1.H12

Thanks for any input.


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