Restrains positions issue of metal ions in protein active site

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GROMACS version:2021
GROMACS modification: Yes/No
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Hi all,
I have prepared my metalloprotein-inhibitor model with CHARMM-GUI and need to restrains positions of Zn atoms. I have tried two different methods and got the same error for both of them:

  1. Adding these lines into ZN2.itp file in toppar folder:
    #ifdef POSRES_ZN
    [ position_restraints ]
    ; i funct fcx fcy fcz
    10952 1 1000 1000 1000
    10953 1 1000 1000 1000
    #endif
  2. Adding these lines into topol.top file:
    ; Include forcefield parameters
    #include “toppar/forcefield.itp”
    #include “toppar/PROA.itp”
    #include “toppar/ZN2.itp”
    #ifdef POSRES_ZN
    #include “posre_zn.itp”
    #endif
    #include “toppar/LHK.itp”
    #include “toppar/SOD.itp”
    #include “toppar/CLA.itp”
    #include “toppar/TIP3.itp”

ERROR 1 [file ZN2.itp, line 22]:
Atom index (10952) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
“position_restraints”
in a part belonging to a different molecule than you intended to.
In that case move the “position_restraints” section to the right molecule.

Any help/suggest will be appreciated
Bests
Zahra

2

Hi Zahra,

Based on the error, it seems that your ZN2.itp has just one atom (or perhaps two atoms) defined in the [ atoms ] section following the [ moleculetype ] with zinc ions. In that case, you should use numbering from that [ atoms ] section, so if there are two atoms, use 1 and 2 instead of 10952 and 10953.

Note that [ atoms ] for each molecule defined in the topology have to have numbering starting with 1, so even if your ZN2.itp has different numbers, make sure to renumber it.

(This is all assuming that adding position restraints to zinc atoms only is what you want to do - keep in mind it will restrain them to their spatial location, but other parts of the system will be able to move freely.)

Best,
MW

3

Dear Milosz,
Hi. Thank you so much for your reply. I have used the following command line to make posre_ZN.itp file so 10952 and 10953 are related to Zn atom numbers in .gro file:
gmx genrestr -f step3_input.gro -o posre_ZN.itp -fc 1000 1000 1000

in ZN2.itp there is only one atom:
[ moleculetype ]
; name nrexcl
ZN2 1

[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 ZN 751 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0
So I have changed it to:
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 ZN 751 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0
2 ZN 752 ZN2 ZN 1 2.000000 65.3700 ; qtot 2.0

#ifdef POSRES_ZN
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
2 1 1000 1000 1000
#endif

Using above mentioned ZN2.itp, I got this issue at the minimization step:
Fatal error:
number of coordinates in coordinate file (step3_input.gro, 132816)
does not match topology (topol.top, 132818)

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Can you please let know how to fix this issue.
I appreciate your time and consideration
Bests
Zahra

4

Hi Zahra, if your ZN2.itp only had 1 atom, then it could be fine too - the name was ambiguous as there’s a ZN2 residue but that could also be 2x ZN.

Now that you made a ZN2 molecule that has two atoms in it, your [ system ] directive probably contains this molecule twice, so grompp will think there are 2x2 = 4 Zn ions while your .gro has only 2. Either decrease the number of ZN2 molecules in [ system ] or make your ZN2 with one atom only.