Hi
I am make parameters for a modified methionine residue - I follow the
tutorial and use their mem.lib for my protein just to observe if it works.
For the modified histidine there is no problem but I get the warning/error
at the end that
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
MEM 3
which corresponds to my 3 modified MEM residues. If I try to look at the pdb
file from the prm and inpcrd
$AMBERHOME/exe/ambpdb -p nir_vac.prmtop < nir_vac.inpcrd > test.pdb
I get the residue correctly placed and no TER added to the pdb file. When I
use the desc MEM I get the following which should be the correct
connectivity
desc MEM
UNIT name:
Head atom: .R<MEM 92>.A<N 1>
Tail atom: .R<MEM 92>.A<C 5>
Contents:
R<MEM 92>
How to resolve the error message?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 17 2010 - 12:00:04 PDT
