Energy minimization gives broken resides

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1

GROMACS version: 2022
GROMACS modification: No
Here post your question
I tried to minimized the structure obtained from Modeller.
Here is the min.mdp:

cpp = /lib/cpp
;define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = -1
;
; Energy minimizing stuff
;
emtol = 500
emstep = 0.001

nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no

cutoff-scheme = verlet

There is no error during the minimization process but when I checked the pdb file generated via trjconv (I did add the -pbc option and most chains were whole), there are some broken resides like a Gly went through the Phe ring.

image
image710×713 143 KB

How can I fix this? Thanks for any help.

2

Not seeing the bond in the visualization software doesn’t necessarily mean it’s missing, sometimes the software just isn’t able to visualize it. Bond Dissappearing in VMD

3

I understand but this topology is still not allowed, is it?
I want to know is there a way to avoid from getting this kind of problematic structure…
Thanks for your replying.

4

The topology is fine but you appear to have a polypeptide backbone passing through a Try ring, which is obviously impossible. If you have modeled in some portion of this structure, revisit how you built it and better optimize sidechain rotamers or any other part of the structure that was built in.