<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear All,<br>
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:<br>
<br>
WARNING: atom HH/HT is missing in residue PAA 93 in the pdb file<br>
You might need to add
atom HH to the hydrogen database of residue ----- in the file ff???.hdb<br>
WARNING: atom NA10 is missing in residue Pol 94 in the pdb file<br>
<br>
Atoms HH and HT are head and tail of the polymer.<br>
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.<br>
What will be the problem? Do I need to specify the atoms in any other files?<br>
Thanking you in advance and waiting for your kind reply.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
India<br>
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