[gmx-users] DSSP problem

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 23 11:11:38 CET 2003

On Wed, 2003-01-22 at 19:57, MOLTENI at unisi.it wrote:
> Hi all
> I have a problem with the "do_dssp" GROMACS module on one of my MD
> trajectories: it is a 8 ns trajectory of a peptide in water and, when I
> run do_dssp on it, the output displays only the first 4440 ps (and the
> program says "last frame: time 4440"), while when I run g_rms on the
> same trajectory file, the output displays the whole 8 ns trajectory. Can
> it be a problem due to file size, since it seems similar to the one
> described in one of the recent e-mails I read on the list (two different
> programs behave differently on the same file...)? 
> some details:
> * the size of my file is 975.284 Mb (so, at least it isn't a "2 Gb
> problem"..)
File size is not the problem. Can you run the dssp in parts? 
E.g. do_dssp -b 5000? 
Do you see anything strange in the RMSD at 4400? It could be that dssp
crashes for some reason, and that the program halts for that reason.

> * I run do_dssp this way: 
> do_dssp -f trajectoryfile -s ....md1.tpr -o ss.xpm -dt 30
> and, as "group" I select the whole "protein" (without the solvent) 
This is correct
> By the way, is it ok to use always the .tpr file of the first MD run (it
> should be the one related to the initial structure of the trajectory, if
> I understand well) in case of multiple runs, for this kind of analysis
> programs? 
Yes, the tpr is only used for atom names here.

For most analysis it is necessary that tpr and xtc match exactly
(watchout when using grompp -shuffle). For some analysis it doesn't
matter, as long as the part you are analyzing is compatible. There is no
good error checking though.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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