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

[Simon Kit Sang Chu]

Hi Mark,

Thanks for your prompt reply. What surprises me is that a change of "define
= POSRES" could cause a problem. The full output from grompp is -

checking input for internal consistency...
calling cpp...
cpp: error: POSRES: No such file or directory
cpp: warning: ‘-x c’ after last input file has no effect
cpp: fatal error: no input files
compilation terminated.
cpp exit code: 1024
Tried to execute: 'cpp  -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top
POSRES p1p2.top > gromppDTyNuM'
The 'cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (npt.gro, 74787)
             does not match topology (p1p2.top, 0)


The additional information is attached here as a reference.

*chainA-pace.top*
[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
     1         N+      1    MET      N      1        0.7         17   ;
qtot 0.7
.
.
.
  919   922   921   920     2    0.0  300.0

; Include Position restraint file
#ifdef POSRES
#include "chainA_posre.itp"
#endif


*chainA_porse.itp*
; position restraints for r_1-62_&_Backbone of FullP1P2 in water

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
.
.
.
 523    1       1000       1000       1000
 530    1       1000       1000       1000

Simon


2017-06-07 16:28 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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
> > --
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