[gmx-users] grompp in gromacs-4.0.4

[S. Vaitheeswaran]

Dear gromacs users,

I am trying to calculate the PMF along the end-to-end distance for a short
polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4.  I run
grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top,
where sd.mdp is:
************************
title               =
cpp              =  /usr/bin/cpp
integrator      =  sd
dt                  =  0.002  ; [ps]
nsteps           =  1000000
nstcomm             =  10     ; frequency for center of mass motion removal
comm_mode           =  Linear ; Remove center of mass translation
comm_grps           =  system
nstxtcout           =  10000  ; frequency to write coordinates to xtc
trajectory
nstxout             =  10000  ; frequency to write coordinates to output
trajectory file
nstvout             =  100000
nstlog              =  10000
nstenergy           =  10000
energygrps          =  6EG    ; group(s) to write to energy file
pbc                 =  no
nstlist             =  0      ; neighbor list is only constructed once and
never updated.
ns_type             =  simple
rlist               =  0      ; cut-off distance for the short-range
neighbor list
rcoulomb            =  0
rvdw                =  0
tc-grps             =  6EG
tau_t               =  0.1    ; [ps]
ref_t               =  300    ; [K]
pull                = umbrella
pull_geometry       = distance
pull_init1          = 0.425   ; [nm]
pull_dim            = Y Y Y
pull_ngroups        = 1
pull_group0         = group 1
pull_group1         = group 2
pull_k1             = 1000
************************
group 1 and group 2 are defined in OH_ends.ndx:
************************
[ group 1 ]
  1  2
[ group 2 ]
  20  21
************************

and 6EG.top is:
************************
#include "ffgmx.itp"
#include "6EG.itp"
[ system ]
Hexa-ethylene glycol: Langevin dynamics
[ molecules ]
6EG               1
************************

But, grompp fails with:
-------------------------------------------------------
Program grompp_s, VERSION 4.0.4
Source code file: readir.c, line: 1013

Fatal error:
Group 6EG not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp.
In that case use the '-n' option.
-------------------------------------------------------

But, I *am* using the -n option!  If I include the group 6EG in the index
file (I didn't think it was necessary since it is defined in the .top file),
grompp chokes with:
"Fatal error: Group group 1 not found in indexfile.", even though group 1 is
defined in the .ndx file.

It works fine without the pulling options.  I have searched the manual, wiki
and mailing list archives for a solution, without success.  This gromacs
newbie is out of ideas -- any help is much appreciated.

thanks,
Vaithee
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