[gmx-users] Structure Breaking during minimization

[Apramita Chand]

Dear All,
I'm trying to incorporate charges and topology obtained from ATB server for
taurine into GROMOS53a6 ff by copying into my local working directory and
adding information in the .rtp file. All other commands work smoothly but
after energy minimzation, except for the NH3+ group, all the other bonds
are broken and individual atoms are just scattered randomly.
What could be the reason?
I have taken the pdb file from ATB server and generated the .itp file too.
>From there, I have taken the charges and the bonded parameters like
bonds,angles I'm assigning the gromos types which are sometimes different
from what has been given in the .itp file. Is it wrong? Should I add new
bonded parameters too in the ffbonded.itp?

Regards,
Apramita