[gmx-users] Problems using grompp and amber force field

TJ Piggot t.piggot at bristol.ac.uk
Tue May 8 03:05:00 CEST 2007


With regards to the versions you are correct, ffamber_v3.3.1 is for use 
with Gromacs 3.3.1. As for the error i would suggest you do what Mark says 
and make sure all your inclusions are correct.  If you still can't find the 
problem then you need to post some of your .top file so we can have a look 
at it


--On 08 May 2007 10:53 +1000 Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> root wrote:
>> Dear GROMACS user:
>> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
>> http://folding.stanford.edu and now I understand your comments.
>> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
>> desapears, but the error messages is similar.
>> (Fatal error:
>>>>> Atoms in the .top are not numbered consecutively from 1
>>>>> -------------------------------------------------------
>>>>> We tested the dick.top file, and we verified that the atoms
>>>>         are numbered
>>>>> consecutively from 1 to 758.)
> Have you inspected the #included files as well? The way cpp works, any
> file #included is literally dropped into its parent file, so if you had
> something wrong in such an #inclusion you'd need to fix that.
> Mark
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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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