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

[Mark Abraham]

Hi,

Yes... if 1UBQ-CG is the coordinates you want the restraints to target.

Mark

On Mon, Jan 14, 2019 at 3:49 PM ZHANG Cheng <272699575 at qq.com> wrote:

> Thank you Mark!
>
>
> The "Protein_A.itp" is obtained by:
> python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp
> ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22
>
>
> So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb".
>
>
> So I should use "-r 1UBQ-CG.pdb"?
> So the whole command is the below?
> gmx grompp -p system.top -r 1UBQ-CG.pdb -c solvated.gro -f
> minimization.mdp -o minimization.tpr
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng"<272699575 at qq.com>;
> Date:  Mon, Jan 14, 2019 10:16 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Re: How to use "define = -DPOSRES" in Gromacs 2018?
>
>
>
> 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?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>