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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
residue.
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.
Armin
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Received on Sun Feb 22 2004 - 04:53:00 PST
