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

[chris.neale at utoronto.ca]

It is not clear to me why you experience this problem. Perhaps post  
your full .top file with .itps and your command line usage.

I did do a search for you suggesting that grompp does not like to find  
ions after solvent and might produce such an error message if it does:
http://www.mail-archive.com/gmx-users@gromacs.org/msg01246.html

So, do you get this error only after adding ions?
If not, please also verify that you get your error in vaccuo.

Note also that 8 heavy atoms in a chargegroup is unusually large and  
may cause you other problems later on.

Chris.

-- original message --

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,