[gmx-users] identifying terminal residue error

gromacs query gromacsquery at gmail.com
Sun Dec 20 22:13:15 CET 2015

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.

DC (169th residue)
DG (so on......)
DC (189th residue)
AX (moldified 190th residue)

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
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

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