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

[Simon Kit Sang Chu]

Hi Mark,

I think I solved the problem. It should be DPOSRES instead of POSRES. The
define command should be implemented as "define = -DPOSRES". Finally, the
chainX_porse.itp should be included in the master topology file, not
chainX-pace.top.

Thanks again by the way.

Simon

2017-06-07 19:18 GMT+08:00 Simon Kit Sang Chu <simoncks1994 at gmail.com>:

> 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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