[gmx-users] bond managment in grompp

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 21 16:18:52 CET 2012

On 22/03/2012 1:46 AM, francesco oteri wrote:
> Dear gromacs user,
> I noted a strange behavior in topology generation workflow.
> I have a protein whose active site contains a Ni atom linked to 4 Cys.
> I inserted the 4 bonds by specbonds.dat.   When I run pdb2gmx, I have 
> inspected
> the Linking messages and they fit with the expected topology, I mean 
> pdb2gmx
> correctly detects the four bonds nickel-sulphur.
> So I run grompp and the topol.tpr has been correctly generated.
> Then I compared topol.top and topol.tpr bonds and I noticed that in 
> topol.top there a lot
> of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium.

Can you show an example of what you interpret as a fake bond?


> I dumped topol.tpr through gmxdump, and I noticed that these bonds are 
> no more present
> and only  "right" bonds are present.
> So, I am wondering why the fake bonds are inserted in topol.top and 
> how grompp detectes
> these bonds.
> Francesco

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