[gmx-users] Residue id of capped peptide getting changed when adding molecules
cy16f01.dilip at nitk.edu.in
Thu Nov 15 06:39:33 CET 2018
I have a capped peptide (ACE-ALA-NME) and now when i add the other
molecules through the command "gmx insert-molecules", the residue id of the
capped peptide, which was 1 as:
gets changed to 1,2 and 3 as in:
4XYZ C1 and so on...
1] How can i prevent the residue id's from getting changed..??(or) retain
their residue id's..?
2] Since when residue id's gets changed, it is treated as different
chains/molecules and bonds between them are shown as
"Warning) Unusual bond between residues: 1(none) and 2 (protein)
Warning) Unusual bond between residues: 2 (protein) and 3 (none)" when
viewed in VMD. causing a problem...
Any suggestions are highly appreciated.
With Best Regards,
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