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
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