[gmx-users] Using specbond.dat in pdb2gmx

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 19 20:49:23 CEST 2014

We can't say without seeing your full command line and at least the termini
of your input file....


On Thu, Jun 19, 2014 at 7:28 PM, Matthew Stancea <mstancea at ggc.edu> wrote:

> >>> Ah, because it's Amber.  Amber force fields are special and have
> specific
>  nomenclature that signifies N- and C-termini, so they automatically get
> built.
>  Changing the residue names by removing the N and C prefixes should fix
> things.
> >> Okay, which file do I remove the N and C prefixes from?
> >Coordinate file, always manipulate the coordinate file.
> >But the fact that you're asking this tells me that likely you never
> actually
> added those prefixes, so pdb2gmx is being "smart" and adding them for you.
>  In
> that case, there's nothing you can do short of (1) modifying the pdb2gmx
> code,
> (2) manually hacking the topology - ugly, but effective, or (3) using a
> different force field that doesn't have terminus-specific naming (anything
> that's not Amber).
> After discussing it with my professor, he believes that I can attempt both
> (2) and (3) until one of them works. Currently, he and I are going through
> the process of designing a script to perform (2).
> Additionally, he told me that the only forcefields other than amber99sb
> that I can try are charmm27 and opls-aa. However, when I attempted to use
> either of those forcefields (these times I was relieved to finally see the
> option to select "none" for the termini), I received this error message:
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 4.6.2
> Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c,
> line: 1109
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your
> coordinate file, add a new terminal database entry (.tdb), or select the
> proper existing terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Does this have to do with the fact that I did select "none" for both
> terminals both of the times?
> Matthew
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