[gmx-users] pdb2gmx fails because of imaginary "Residue E"

kolnkempff kolnkempff at gmail.com
Sun Dec 1 17:07:16 CET 2013

Thanks Justin, I appreciate your patience with newbie questions.

When I realign columns, I get:
Fatal error:
Atom H in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.

So I tried the flag -ignh which produced:
Fatal error:
Atom C in residue NME 3 was not found in rtp entry NME with 6 atoms
while sorting atoms.

So I manually edited the file to include all HC, CT, etc. labels (from
aminoacids.rtp) which produced:
WARNING: there were 6 atoms with zero occupancy and 23 atoms with
         occupancy unequal to one (out of 32 atoms). Check your pdb file.
Identified residue PHE0 as a starting terminus.
Identified residue NME0 as a ending terminus.
Fatal error:
Atom CT in residue PHE 0 was not found in rtp entry NPHE with 22 atoms
while sorting atoms.

So it seems ACE has been lost.  

Any insight would be greatly appreciated.  Today, I'll try using amberTools
to work with this.


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