[gmx-users] help and a tutorial

Sebastien Gerega seb at gerega.net
Sat Oct 15 09:52:43 CEST 2005

Thanks Tsjerk,
I have been looking at the your mdcourse and it looks like it will be 
very helpful.
However, back to my current problem...
I do not get any "long bond" warnings but I do have CA not found trying 
to use CA2+ warnings - which I don't think matter...
and I got a warning saying "there were 0 atoms with zero occupancy and 3 
atoms with occupancy unequal to one (out of 1334 atoms)
is that warning a problem?
Finally I got a warning saying that CB is missing in residue LEU 1 in 
the pdb file.
I had to use the -missing argument ot get past that warning...

Would any of these warnings result in my error? If it is just because I 
docked the proteins and there are now overlpas, is there away to get 
past this problem?

Tsjerk Wassenaar wrote:

> Hi Sebastien,
> We meet again :)
> For a general tutorial on MD you can walk through the one at 
> http://md.chem.rug.nl/education/mdcourse2004/
> There is another one specifically on setting up systems of a protein 
> and ligand, which may also be interesting to you, but for these I 
> don't know the sites.
> If you meet any problems directly related to the tutorial, you can 
> also contact me, as I'm for the greater part responsible for that site 
> (and I really need to revise it  ;)).
> The 1-4 interaction either means that you have overlaps due to the 
> docking process which cause the system to explode, or a faulty 
> topology. If the latter is the case you would probably have had a 
> 'long bond' warning when running grompp.
> Cheers,
> Tsjerk
> On 10/12/05, *Erik Lindahl* <lindahl at sbc.su.se 
> <mailto:lindahl at sbc.su.se>> wrote:
>     Hi Sebastien,
>     On Oct 12, 2005, at 5:25 AM, Sebastien Gerega wrote:
>>     Hi all,
>>     I am pretty new to Gromacs and MDS in general... I am trying to
>>     run a simulation on a docked system (
>>     http://www.members.optushome.com.au/sebkg/test.pdb) and have
>>     tried several variations of what seem to be pretty standard
>>     settings to me but when I go to run the EM I get the following:
>>     step 0 warning: 1-4 interaction between 725 and 730 at a distance
>>     1.842 which is larger than the 1-4 table size 1.000 nm
>>     These are ignored for the rest of the simulation
>>     This usually means your system is exploding, if not, you should
>>     increase table-extension in your mdp file
>>     Step 1 Warning: pressure scaling more than 1%, mu: 1.02036
>>     1.02036 1.02036
>>     Segmentation fault
>     It's described in more detail here:
>     http://www.gromacs.org/faq/index.php#1-4cut
>     Cheers,
>     Erik
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> -- 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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