[gmx-users] Warning: Short Bond pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I did 50ns MD simulation of a protein-ligand complex. From this trajectory,
I extracted region of trajectory having stable rmsd and generated an
average structure. I want to run this average structure to get an idea of
setting some restraints. but when I do gmx pdb2gmx I get following warning:-

Warning: Short Bond (9-10 = 0.042416 nm)
Warning: Short Bond (9-11 = 0.0463433 nm)
Warning: Short Bond (9-12 = 0.0452425 nm)
Warning: Short Bond (13-14 = 0.0407501 nm)
Warning: Short Bond (13-15 = 0.0425715 nm)
Warning: Short Bond (13-16 = 0.0421154 nm)
Warning: Short Bond (65-66 = 0.0418464 nm)
Warning: Short Bond (65-67 = 0.0454554 nm)
Warning: Short Bond (65-68 = 0.0438005 nm)
Warning: Short Bond (103-105 = 0.0498706 nm)
Warning: Short Bond (103-106 = 0.0482166 nm)
Warning: Short Bond (161-162 = 0.0384303 nm)
Warning: Short Bond (161-163 = 0.0395632 nm)
Warning: Short Bond (161-164 = 0.0404804 nm)
Warning: Short Bond (178-179 = 0.0379231 nm)
Warning: Short Bond (178-180 = 0.0350074 nm)
Warning: Short Bond (178-181 = 0.0367544 nm)
Warning: Short Bond (195-197 = 0.0491068 nm)
Warning: Short Bond (240-241 = 0.0410752 nm)
Warning: Short Bond (240-242 = 0.0400188 nm)
Warning: Short Bond (240-243 = 0.0389276 nm)
Warning: Short Bond (244-245 = 0.0395354 nm)
Warning: Short Bond (244-246 = 0.0394185 nm)
Warning: Short Bond (244-247 = 0.0411173 nm)
Warning: Short Bond (254-255 = 0.0496385 nm)
Warning: Short Bond (254-256 = 0.0490917 nm)
Warning: Short Bond (254-257 = 0.0487225 nm)
Warning: Short Bond (320-321 = 0.0389006 nm)
Warning: Short Bond (320-322 = 0.0354672 nm)
Warning: Short Bond (320-323 = 0.0318275 nm)
Warning: Short Bond (332-333 = 0.044048 nm)
Warning: Short Bond (332-334 = 0.0431301 nm)
Warning: Short Bond (332-335 = 0.0443143 nm)
Warning: Short Bond (339-340 = 0.0436942 nm)
Warning: Short Bond (339-341 = 0.044572 nm)
Warning: Short Bond (339-342 = 0.0438389 nm)
Warning: Short Bond (386-387 = 0.0485982 nm)
Warning: Short Bond (386-388 = 0.0493432 nm)
Warning: Short Bond (400-401 = 0.0365161 nm)
Warning: Short Bond (400-402 = 0.0400003 nm)
Warning: Short Bond (400-403 = 0.038517 nm)
Warning: Short Bond (552-553 = 0.0489085 nm)
Warning: Short Bond (552-554 = 0.0483887 nm)
Warning: Short Bond (552-555 = 0.0498913 nm)
Warning: Short Bond (556-557 = 0.0345456 nm)
Warning: Short Bond (556-558 = 0.0396005 nm)
Warning: Short Bond (556-559 = 0.0370519 nm)
Warning: Short Bond (575-576 = 0.0458407 nm)
Warning: Short Bond (575-577 = 0.0455252 nm)
Warning: Short Bond (575-578 = 0.0448519 nm)
Warning: Short Bond (664-665 = 0.0423401 nm)
Warning: Short Bond (664-666 = 0.0390075 nm)
Warning: Short Bond (664-667 = 0.0406177 nm)
Warning: Short Bond (671-672 = 0.0369435 nm)
Warning: Short Bond (671-673 = 0.0354056 nm)
Warning: Short Bond (671-674 = 0.0373171 nm)
Warning: Short Bond (725-726 = 0.0389842 nm)
Warning: Short Bond (725-727 = 0.0393952 nm)

I understand that the average structure is not necessarily anything
physically meaningful but how I assume that it can give the equilibrium
values to set the restraints.
I need your help to figure out this warning, please.
Thanks in advance.
Sadaf