[gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

[Mark Abraham]

On 13/10/2011 8:16 PM, Ahmad Randy wrote:
> Hi All,
>
> I understand that there were already some discussions about new DSSP 
> exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it 
> true that this two DSSP and do_dssp do not compatible each other?

If the new DSSP requires the code in do_dssp to be updated, that hasn't 
happened, and likely won't happen for a while. If someone can 
substantiate that it needs a change, and file a GROMACS Redmine issue 
describing what needs to happen, then it will be considered for the 4.6 
release.

>
> I was running in Ubuntu 10.04, and this is what I got:
>
> do_dssp -f 300K.trr -s 300K.tpr -o dssp
>
> I choose 5 'Mainchain'
>
> Fatal error:
> Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ 
> ddvDjL4J > /dev/null 2> /dev/null
>
>
> I already set the "export DSSP=/home/madndy/dssp/dssp", and also try 
> the latest do_dssp.c (from gromacs-4.6) file for instalation. Still 
> didn't work.
>
> Are there are any suggestion or correction in my step? Or what version 
> of gromacs that work well with DSSP? Or should I get the older version 
> of DSSP that work with do_dssp?

I think that is the most reliable approach.

> And where can I find the older version of DSSP because I can't find 
> the older version in: http://swift.cmbi.ru.nl/gv/dssp/ .

They say it is available. Please ask them.

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111014/83c7bd1c/attachment.html>