Hi,
by looking into the code I could figure out some things.
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
This warning comes from the -rmsmin option which is set to 0 by default and
which controls the structure output.
The problem with tpr/gro files is that g_cluster uses mass weighted RMSD
calculation by default and if there are no masses (as in the gro file), it
tries to assign masses from the atom name. This lead to masses of around 200
for H atoms which are called HG*, the program assumed this was mercury!
So I'd strongly advise everybody to use tpr files within g_cluster. It would also be nice
to insert a warning in g_cluster if atoms other than C, O, N, H, S are "found".
Cheers
Sabine
On 05/14/2013 06:06 PM, Mark Abraham wrote:
Hi,
I don't know. I don't know how to trigger it, and nobody has said how they
triggered it :-)
Mark
On May 14, 2013 4:45 PM, "Preeti Choudhary" <
[email protected]> wrote:
should we worry about the warning ???
On Tue, May 14, 2013 at 7:19 PM, Mark Abraham <[email protected]
wrote:
We'd need a lot more info to start to understand why .tpr vs .gro
does/should affect the result (or not)!
Mark
On May 14, 2013 2:32 PM, "Sabine Reisser" <[email protected]>
wrote:
Hi,
I'm having the same warning, would also be interested in what it means.
Additionally, I get different results if I use a tpr instead of a gro
file
in the -s option, using the same trajectory with -f. The results are
completely different, for the gro file I get 42 while for the tpr file
I
get 2 clusters.
Does anybody know why this is the case?
Cheers
Sabine
On 05/10/2013 04:33 PM, Preeti Choudhary wrote:
hello everyone
I am trying to cluster my data using g_cluster.I simulated the whole
protein. I did the g_cluster analysis with only certain region of the
protein which I specified using an index file.The program runs fine
and
gives 1 cluster.My concern is the warning it gives which states that
:-
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
what exactly this warning means ???
-thanks
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