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,
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