[gmx-users] help and a tutorial
seb at gerega.net
Sat Oct 15 09:52:43 CEST 2005
I have been looking at the your mdcourse and it looks like it will be
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
> 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.
> 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:
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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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