[gmx-users] Missing bond

[Sudip Das]

Dear All,

While I am preparing my system topology with pdb2gmx for a system
containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
number of bonds per surfactant molecules, but actually it has 37 bonds
(anyways, the number of angle, dihedral etc. are correct). From the
generated topology for this surfactant, I found out the missing bond. But I
checked that I have incorporated that bond in aminoacids.rtp file and that
bond type is also present in the ffbonded.itp file.

To figure out the reason, I used the pdb2gmx for a system with only 30
surfactant molecules in water (no enzyme). Again I encountered the same
problem.

So, what could be the solution? Please assist me.

Thanks in advanced.


Best regards,
Sudip