# Using specbond.dat to define Zn-Cys bonds

**URL:** <https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106>\
**Category:** User discussions\
**Created:** [May 6, 2021, 6:49am UTC](https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106 "2021-05-06T06:49:00Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![rcrehuet](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rcrehuet/32/340_2.png) [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\
**Post date:** [May 6, 2021, 6:49am UTC](https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106/1 "2021-05-06T06:49:00Z")

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GROMACS version: 2019  
GROMACS modification: Yes with plumed

Hi all,  
I would like to simulate a protein containing a Zn ion bound to 4 Cys. After reading the `pdb2gmx input files` section in the gromacs documentation and looking for similar cases in the gromacs mailing list/forum I tried the following approach:

1. Separate the protein residues and the Zn residue in pdb file with a TER line, so that termini are correctly identified.
2. Merge the 2 chains with the `-merge interactive` option of pdb2gmx.
3. Add a line `ZN2 Protein` to `residuetypes.dat` in the force field folder.
4. add a line `CYS SG 2 ZN ZN2 4 0.234 CYN ZN2` to `specbond.dat` in the current folder, where the pdb file also resides (the documentation is not clear about where specbond.dat file should reside.)

There are a couple of things (probably related) that don’t work as expected.  
First, when running pdb2gmx I get this warning:

```auto
Warning: No residues in chain starting at ZN21201 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

```

But ZN2 is defined in residuetypes.dat. So why does this appear?

Second, when pdb2gmx prints the `Special Atom Distance matrix:` ZN is not shown (only CYS-CYS distances), and when checking `topol.top`, no bond has been created between ZN and the CYS residues, and the latter have not been renamed as CYN.

I’ve checked, and in the pdb file, the ZN–SG distances are: 0.225, 0.253, 0.211 and 0.247 nm. So they are within 10% of the distance specified in the `specbond.dat`. Why aren’t these bonds created then and how should I define them or format the pdb so that they are created?

Thanks for your time.

Best,  
Ramon

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [May 10, 2021, 7:58am UTC](https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106/2 "2021-05-10T07:58:23Z")

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Hi,  
An alternative is to apply simple harmonic restrain between the two atoms (Zn and SG) : use `[bonds]` type 6 in the `[moleculetype]` section in the topology file.

See the following table for the synthax [http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topfile](http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topfile)

Best regards  
Alessandra

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**Author:** ![rcrehuet](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rcrehuet/32/340_2.png) [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\
**Post date:** [May 13, 2021, 1:16pm UTC](https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106/3 "2021-05-13T13:16:12Z")

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Thanks, Alessandra. That is a clever option. However, I would still like to see how this could be done with `specbond.dat` as I really think that would be the most automatic or canonical way to do it, and I really don’t see how it works because the documentation is very sparse.  
Best regards,  
Ramon

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<div class="post-metadata">

**Author:** ![rcrehuet](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rcrehuet/32/340_2.png) [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\
**Post date:** [May 14, 2021, 7:33am UTC](https://gromacs.bioexcel.eu/t/using-specbond-dat-to-define-zn-cys-bonds/2106/4 "2021-05-14T07:33:15Z")

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Hi,  
I found out the problem. It was very silly! In the `specbond.dat` I was using first the atom name and then the residue name (which are very similar for Zn) and it should be the opposite. That is why it never found a satisfying distance. Now it works.  
Best regards,  
Ramon