Error in Restraining the Ligand

User discussions
,
1

GROMACS version:2022
GROMACS modification: Yes/No
Here post your question
I am getting error in Equlibration stage:
command: gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tp
error message: ERROR 1 [file GP001.itp, line 496]:
No default Position Rest. types

ERROR 2 [file GP001.itp, line 497]:
No default Position Rest. types

ERROR 3 [file GP001.itp, line 498]:
No default Position Rest. types

ERROR 4 [file GP001.itp, line 499]:
No default Position Rest. types

ERROR 5 [file GP001.itp, line 500]:
No default Position Rest. types

ERROR 6 [file GP001.itp, line 501]:
No default Position Rest. types

ERROR 7 [file GP001.itp, line 502]:
No default Position Rest. types

ERROR 8 [file GP001.itp, line 503]:
No default Position Rest. types

ERROR 9 [file GP001.itp, line 504]:
No default Position Rest. types

ERROR 10 [file GP001.itp, line 505]:
No default Position Rest. types

ERROR 11 [file GP001.itp, line 506]:
No default Position Rest. types

ERROR 12 [file GP001.itp, line 507]:
No default Position Rest. types

ERROR 13 [file GP001.itp, line 508]:
No default Position Rest. types

ERROR 14 [file GP001.itp, line 509]:
No default Position Rest. types

ERROR 15 [file GP001.itp, line 510]:
No default Position Rest. types

ERROR 16 [file GP001.itp, line 511]:
No default Position Rest. types

ERROR 17 [file GP001.itp, line 512]:
No default Position Rest. types

ERROR 18 [file GP001.itp, line 513]:
No default Position Rest. types

ERROR 19 [file GP001.itp, line 514]:
No default Position Rest. types

ERROR 20 [file GP001.itp, line 515]:
No default Position Rest. types

ERROR 21 [file GP001.itp, line 516]:
No default Position Rest. types

ERROR 22 [file GP001.itp, line 517]:
No default Position Rest. types

ERROR 23 [file GP001.itp, line 518]:
No default Position Rest. types

ERROR 24 [file GP001.itp, line 519]:
No default Position Rest. types

ERROR 25 [file GP001.itp, line 520]:
No default Position Rest. types

ERROR 26 [file GP001.itp, line 521]:
No default Position Rest. types

ERROR 27 [file GP001.itp, line 522]:
No default Position Rest. types

ERROR 28 [file GP001.itp, line 523]:
No default Position Rest. types

ERROR 29 [file GP001.itp, line 524]:
No default Position Rest. types

ERROR 30 [file GP001.itp, line 525]:
No default Position Rest. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘GP001’

turning H bonds into constraints…

Excluding 2 bonded neighbours molecule type ‘SOL’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘NA’

turning H bonds into constraints…

Setting gen_seed to -574652421
Need help in this

2

You probably haven’t defined the restraints properly. Have a look at File formats - GROMACS 2024.4 documentation.

What do your position restraints look like? (You only have to post a line or two, not all ~30).

3

Thank you for the reply. I will check this, but can’t i proceed without restraining step?

4

Sure, check your GP001.itp file. The restraints are specified in there, probably through an #ifdef POSRES statement. You can decide to remove those lines or to remove -DPOSRES from define in the mdp file. However, it’s often a good idea to restrain most molecules, except the solvent, during energy minimization and the first equilibration stage(s).

5

yes, i just checked and got them in .itp file. Thank you once again!