[gmx-users] identifying terminal residue error

[gromacs query]

Hi All

I have a modified base in normal DNA chain. Thus I added that residue in
rtp file and updated residuetypes.dat as well (CHARMM36). When I use pdb2mx
with -ter interactive mode then it wrongly identifies the ending terminal
at the residue just before the modified base. e.g.


:
:
TER
DC (169th residue)
DT
DG (so on......)
DC (189th residue)
AX (moldified 190th residue)
.
.
DA
DG
TER
:
:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Warning message:

Identified residue DC169 as a starting terminus.
Warning: Residue AX190 in chain has different type (Other) from starting
residue DC169 (DNA)..

More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue DC189 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for DC-169
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

So its wrongly identifying DC as ending terminal. Not sure what else needs
to be modified as residuetypes.dat has been updated too in my local
directory. I dont have any new type of connection between modified base and
normal base.

Thanks for any help