[gmx-users] Error: Atoms in the .top are not numbered consecutively

[Henri K. Ervasti]

Dear all,

There was already a similar topic in the archive, but it didn't apply to
my case. So, could you help me with the following problem? For some
reason when I try to grompp my input, it gives the following error:

Program grompp, VERSION 3.3.2
Source code file: toppush.c, line: 835

Fatal error:
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr
= 4, while at->nr = 2)

While my input in the .top for the molecule looks like this:

[ moleculetype ]
; Name nrexcl
NFM      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CS1     1  NFM      C1     1   -0.048  12.0110  
     2       CS2     1  NFM      C2     1    0.321  12.0110 
     3        OE     1  NFM      O3     1   -0.448  15.9994 
     4       CS2     1  NFM      C4     1    0.222  12.0110 
     5       CS1     1  NFM      C5     1    0.135  12.0110 
     6      NR6*     1  NFM      N6     1   -0.053  14.0067 
     7         C     1  NFM       C     1    0.344  12.0110 
     8         O     1  NFM       O     1   -0.519  15.9994 
     9       HA1     1  NFM      H1     1    0.000   1.0080
    10       HA1     1  NFM      H2     1    0.000   1.0080
    11       HA2     1  NFM      H3     1    0.000   1.0080
    12       HA2     1  NFM      H4     1    0.000   1.0080
    13       HA2     1  NFM      H5     1    0.000   1.0080
    14       HA2     1  NFM      H6     1    0.000   1.0080
    15       HA1     1  NFM      H7     1    0.000   1.0080
    16       HA1     1  NFM      H8     1    0.000   1.0080
    17       HCO     1  NFM      H9     1    0.046   1.0080

So, everything in correct order. I don't understand why it produces this
error message. I tried with a simple test case with water and that
worked fine, although it has only 3 atoms, so the error is not produce,
maybe because there is something strange starting from atom number 4. I
tried to change the order of the atoms etc, but the error always comes
on the same spot. If I change the nr. 4 to 5, then I get the same error,
but with 5. If I change a number from before, like 2 to 1, it gives the
error from that position, so it works fine until the 4th position.

Another note here that when I run this on my laptop (Mac), it works
fine, but not on my desktop (Fedora Core 10).

I'm rather baffled by this, and any help would be greatly appreciated!

Yours,
Henri