[gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences

[fulvio ciriaco]

Hello,
I have to simulate some non natural sequences containing sometimes both
T and U nucleic acids.
However pdb2gmx incorrectly detects the terminus, i.e., for a sequence like
TCAUA
it says
Identified residue DT1 as a starting terminus.
Warning: Residue RU4 in chain has different type (RNA) from starting 
residue DT1 (DNA).
Warning: Residue DA5 in chain has different type (DNA) from starting 
residue DT1 (DNA).
Identified residue DA3 as a ending terminus.

Then it does not treat DA5 as a ending terminus, i.e. , with 
amber99sb-ildn ff
Fatal error:
Atom H3T in residue DA 5 was not found in rtp entry DA with 32 atoms
while sorting atoms.

Is there some way to circumvent the excessive knowledge pdb2gmx has of 
biological
systems?

I attach the tertiary structure for one such sequence.

Fulvio