I'm getting following error while pdb2gmx:
Residue 2 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Pls help!
yes sir there were some missing atoms and some to be renamed. Thanks.
Hi Anwesh,
It sounds like you are missing an atom in your input file, specifically the second carbon in the sidechain of that specific lysine.
In amber99sb-ildnp the atoms are named as follows for lysine. Hopefully this gives you an idea of how the atoms are named relative to the structure:
LYS N
LYS H
LYS CA
LYS HA
LYS CB
LYS HB1
LYS HB2
LYS CG
LYS HG1
LYS HG2
LYS CD
LYS HD1
LYS HD2
LYS CE
LYS HE1
LYS HE2
LYS NZ
LYS HZ1
LYS HZ2
LYS HZ3
LYS C
LYS O
It is also possible that your input file simply has different atom names, and all you would have to do is rename it (using sed/awk) to the appropriate one and it should work.
yes sir there were some missing atoms and some to be renamed. Thanks.
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