[gmx-users] WARNING: atom missing

Rahul Karyappa r.karyappa at ncl.res.in
Wed Aug 24 13:39:07 CEST 2005

Dear All,

    I have a .pdb file containing two residues. One of
which is Sodium ions. I entered all the atoms in the .rtp file. When I
ran pdb2gmx command it gave me following warnings:

WARNING: atom HH/HT is missing in residue PAA 93 in the pdb file

         You might need to add
atom HH to the hydrogen database of residue ----- in the file ff???.hdb

WARNING: atom NA10 is missing in residue Pol 94 in the pdb file

Atoms HH and HT are head and tail of the polymer.

It gave me this warning for all the Sodium atoms. Then I ran pdb2gmx
with -missing command. It worked and I got the .gro and .top files.

   What will be the problem? Do I need to specify the atoms in any other files?

Thanking you in advance and waiting for your kind reply.

Rahul Karyappa

NCL, Pune


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