[gmx-users] DSSP problem

[David van der Spoel]

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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