[gmx-users] number of coordinates does not match after POSRES

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 7 10:28:46 CEST 2017


Hi,

We can't tell, because position restraints are an attribute of
moleculetypes and those are hidden in your itp files and you didn't share
which moleculetype grompp reported was the problem. Please copy and paste
terminal output to make a useful description.

You'll need to include the position restraint file appropriate to each
moleculetype, of course - not the same one each time.

Mark

On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu <simoncks1994 at gmail.com> wrote:

> Hi,
>
> Initially, my topology file can run grompp with .mdp and .gro. However,
> after putting POSRES in my mdp, the warning "number of coordinates does not
> match" and there is no coordinate recognized in my topology file anymore.
> Therefore, the option POSRES somehow changes everything.
>
> The topology file is put here. Is there anything I have written
> incorrectly?
>
> ; Include forcefield parameters
> #include "ffPACE_1.3.itp"
>
> ; Include chain topologies
> #include "chainA-pace.top"
> #include "chainB-pace.top"
>
> ; Include water topology
> #include "cgWater.itp"
>
> ; Include topology for ions
> #include "martini_v2.0_ions.itp"
>
> [ system ]
> ; Name
> FullP1P2 in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_A     1
> Protein_B     1`
> SOL             72899
> NA+             20
> --
> 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.
>


More information about the gromacs.org_gmx-users mailing list