[gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

[Mark Abraham]

Hi,

The purpose of applying position restraints is to restrain the coordinates
to a set of target coordinates. grompp now requires you to be explicit
about what target you choose. You need to decide what they are, and pass
the file containing them to grompp -r.

Mark

On Mon, Jan 14, 2019 at 3:17 PM ZHANG Cheng <272699575 at qq.com> wrote:

> Thank you Mark!
>
>
> Sorry, I do not have a "targetcoords.gro" for the grompp.
>
>
> I was trying to use
> "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o
> minimization.tpr",
> and the "system.top" has a line of " #include "Protein_A.itp" ",
> and the "Protein_A.itp" file has the restraints I need.
>
>
> Should I modify the "minimization.mdp" instead?
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng"<272699575 at qq.com>;
> Date:  Mon, Jan 14, 2019 09:53 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  How to use "define = -DPOSRES" in Gromacs 2018?
>
>
>
> My backbone restraints is shown in the "Protein_A.itp" file:
>
>
>
> #ifdef POSRES
> #ifndef POSRES_FC
> #define POSRES_FC 1000.00
> #endif
>  [ position_restraints ]
>       1    1    POSRES_FC    POSRES_FC    POSRES_FC
>       3    1    POSRES_FC    POSRES_FC    POSRES_FC
>       5    1    POSRES_FC    POSRES_FC    POSRES_FC
> ......
>     162    1    POSRES_FC    POSRES_FC    POSRES_FC
>     163    1    POSRES_FC    POSRES_FC    POSRES_FC
> #endif
>
>
>
>
> The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp
> file for "gmx grompp".
>
>
> However, adding "define = -DPOSRES" to the mdp file causes the error:
>
>
>
>
> Fatal error:
> Cannot find position restraint file restraint.gro (option -r).
> From GROMACS-2018, you need to specify the position restraint coordinate
> files
> explicitly to avoid mistakes, although you can still use the same file as
> you
> specify for the -c option.
>
>
>
>
> The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the
> problem for that?
>
>
> How can I trigger those restraints in "Protein_A.itp" file using Gromacs
> 2018?
> --
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