Hi,
I try to simulate DNA or better parts of a long DNA double-helix.
Therefore, the system I use is not "correctly" terminated at the ends
from chemical point of view with OH-groups but rather cut out the longer
helix. Nevertheless, all residues are named correctly, all atoms needed
in the residues are present and corresponding parameters exist in the
Amber-Forcefield which I intent to use.
When I run pdb2gmx, it always tries to recognize start end ending termini:
Identified residue DG1 as a starting terminus.
Identified residue DC34 as a ending terminus.
and then later on, it fails because the P-Atoms are not found in the rtp
as it searches e.g. in DG5 instead of DG:
Fatal error:
Atom P in residue DG 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.
How can I avoid this error? I tried -noter option but this does not help.
Is there a way to just treat the residues as the occur in the pdb-file
without automatically detection of starting and ending terminus?
Thanks for your help,
Matthias
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