GROMACS version: version 2020.1
GROMACS modification: No
Hi gromacs user!
I am new to gromacs and I am not familiar with the files and sometimes I get a little confused.
I am trying to apply a distance restraint type 6 between an specific ions and some residues of the protein.
In my system I have different group of molecules. The protein present one *.itp file and the ions another *.itp file.
There exist a way to apply the distance restraints not merging the ions in the protein *.itp file.
If is possible how can I define the distance_restraints section? and in which file I have to added?
Inside the protein.itp file I have the distance restraints specified like this:
#ifdef DISRES
[ distance_restraints ]
atom1 atom2 type dist. between atoms force constant
2401 21343 6 3.75 0.0 DISRES_FC
[…]
#endif
- For me atom1 = atom index of a protein residue, and atom2 = atom index of the ion
This way an error appears related to the atom index:
ERROR 1 [file PROA.itp, line 105582]:
Atom index (21343) in distance_restraints out of bounds (1-10671).
This probably means that you have inserted topology section
“distance_restraints”
in a part belonging to a different molecule than you intended to.
In that case move the “distance_restraints” section to the right molecule.
I take a look at the itp files, and I see that they do not correspond to the atomic index, because the atom index corresponds to the ones defined in the pdb file of the total complex.
How can I fix it without merging the two type of molecules in one *.itp file?
It would be grateful if you could help me with this mistake.
Thank you very much in advanced for your help
Regards,
Anna