[gmx-users] Trouble editing mdp file

[Oliver Lange]

Hi,

i have never seen this kind of error, so my guess might be totally wrong:
Are you using a windows based system, or a mix of windows and unix?
Windows has a different code for the end of a line (EOL) it uses Carriag Return (CR) AND 
Line Feed (LF) together, while
Unix uses only LF. If you wrote the file with a windows editor and tried to grompp it 
under unix, grompp would read 'integrator = mdCR'. Which it wouldn't recognize because it 
wants one of md, steep, cg, etc. well you know the list.

Try to use the tool dos2unix which should replace 'CR LF' by 'LF'.

Don't kill me if i am wrong.
Greetings to Australia
Oliver


p.keymer at student.qut.edu.au wrote:
> Hi all
> 
> I am a new gromacs user and I atempting to make changes to 
> the standar mdp file. 
> 
> This is the file i am using:
> 
> ""
> title               =  fws 
> cpp                 =  /lib/cpp 
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002	; ps !
> nsteps              =  50000	; total 100 ps.
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  0
> nstfout             =  0
> nstlist             =  10 
> ns_type             =  grid
> rlist               =  0.9
> coulombtype		=  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing		=  0.12
> fourier_nx		=  0
> fourier_ny		=  0
> fourier_nz		=  0
> pme_order		=  6
> ewald_rtol		=  1e-5
> optimize_fft		=  yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1	0.1
> tc_grps		    =  protein	sol
> ref_t               =  300	300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> ""
> 
> 
> all I doo is change the nsteps and save it then attempt to 
> run grompp.  when I do so the following appears:
> 
> 
> ""
> creating statusfile for 1 node...
> ' for variable integrator, using 'md'
> Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
> ' for variable ns-type, using 'Grid'
> Next time use one of: 'Grid' 'Simple'
> ' for variable coulombtype, using 'Cut-off'
> Next time use one of: 'Cut-off' 'Reaction-
> Field' 'Generalized-Reaction-
> Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User'
> ' for variable optimize_fft, using 'no'
> Next time use one of: 'no' 'yes'
> ' for variable tcoupl, using 'No'
> Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes'
> ' for variable Pcoupl, using 'No'
> Next time use one of: 'No' 'Berendsen' 'Parrinello-
> Rahman' 'Isotropic'
> ' for variable Pcoupltype, using 'Isotropic'
> Next time use one 
> of: 'Isotropic' 'Semiisotropic' 'Anisotropic' 'Surface-
> Tension'
> ' for variable gen-vel, using 'no'
> Next time use one of: 'no' 'yes'
> ' for variable constraints, using 'none'
> Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-
> angles' 'all-angles'
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
> Warning: as of GMX v 2.0 unit of compressibility is truly 
> 1/bar
> checking input for internal consistency...
> ...ling /lib/cpp 
> cpp: error 0: No source file 
> cpp exit code: 2048
>   -I/pkg/gromacs/share/top  pep.top > grompp028037'
> ' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file 
> (after_pr.gro, 2647)
>              does not match topology (pep.top, 0)
> ""
> 
> Please can someone help
> 
> Thank you in advance
> 
> Philip Keymer
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-- 
Oliver Lange
MPI for biophysical Chemistry
olange at gwdg.de
Fax: +495512012302
Tel: +495512012305