As I have to come to Amber9 with pdb files that have passed other software
(DOCK, Chimera, VMD, MM packages) I would like to know which protocol is
followed by Amber9 at present about TER records.
Precisely, which residues are termed ATOM and which ones HETATM, and whether
TER records are always needed to separate different residues if called ATOM,
while not necessary if called HETATM.
For example, a pdb file only containing lipid and water molecules is accepted
by LEaP with ATOM, while Chimera transforms all ATOM recods into HETATM records
and removes all TER records that I had interposed between the lipid and the
water residues. In fact, when LEaP solvates, it adds TER records between the
water residues.
If I remember correctly, recent pdb rules tell that it is technically correct
to remove the TERs between HETATM residues because HETATM residues in PDB
format are not connected to each other unless there are CONECT records that say
the contrary.
To be on the safe side, I always insert TERs. Though, they are removed by other
packages. Luckily there is Python to rearrange the files. Annoying, however,
and not free of problems if one is rushed.
Thanks
francesco pietra
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Received on Sun Nov 25 2007 - 06:07:31 PST
