[gmx-users] Residue id of capped peptide getting changed when adding molecules

Dilip.H.N 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:
    1ACE    CH3
    1ACE   HH31
    1ACE   HH32
    1ACE   HH33
    1ACE      C
    1ACE      O
    1ALA      N
    1ALA     HN
    1ALA     CA
    1ALA     HA
    1ALA     CB
    1ALA    HB1
    1ALA    HB2
    1ALA    HB3
    1ALA      C
    1ALA      O
    1NME      N
    1NME     HN
    1NME    CH3
    1NME   HH31
    1NME   HH32
    1NME   HH33
gets changed to 1,2 and 3 as in:
    1ACE    CH3
    1ACE   HH31
    1ACE   HH32
    1ACE   HH33
    1ACE      C
    1ACE      O
    2ALA      N
    2ALA     HN
    2ALA     CA
    2ALA     HA
    2ALA     CB
    2ALA    HB1
    2ALA    HB2
    2ALA    HB3
    2ALA      C
    2ALA      O
    3NME      N
    3NME     HN
    3NME    CH3
    3NME   HH31
    3NME   HH32
    3NME   HH33
    4XYZ     N1
    4XYZ     N2
    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.
Thank you.

With Best Regards,

Ph.D. Student.

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