[gmx-users] mismatch sol.gro/topol.gro

Dallas Warren dallas.warren at monash.edu
Wed Nov 28 22:10:34 CET 2018


http://manual.gromacs.org/documentation/2018.3/user-guide/run-time-errors.html#number-of-coordinates-in-coordinate-file-does-not-match-topology

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Thu, 29 Nov 2018 at 04:43, Francesco Pietra <chiendarret at gmail.com> wrote:
>
> I am preparing (as a newcomer to gromacs) a complex of a protein with two
> ligands. One is the universal GDP, the other one a diterpenoid. GROMCS2018,
> CGenFF, CHARMM36.
>
> The output of addions complains about GDP.prm (the GDP.str of CGenFF origin
> had no problems for NAMD/CHARMM36) and (because of this, or not) there is a
> mismatch of ion number
> Fatal error:
> number of coordinates in coordinate file (complex_solv.gro, 51025)
>              does not match topology (topol.top, 51137).
>
> Attached the full output. Grateful for advice
> --
> 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