[gmx-users] problem regarding dssp

[sangeeta]

dear Sir,

   Thanks a lot for your reply.I am sorry for the fact that my subject name 
does not tally with the problem I faced.I really apologize for that.
   So I do not need to include explicitely "pbc=xyz" in my .mdp file as it 
is already being used by default.
         
   Regarding dssp I used the following commands
   
   export DSSP=/home/debjani/dssp
   setenv DSSP /home/debjani/dssp
   do_dssp -s md.tpr -f traj.xtc 
      
  At the end of the program only the files namely ddEZ117f ddOWnvlx etc were 
present, but no .xpm files were there.I want to get the plot of changing of 
secondary structural elements during the run.PLease help.

regards
 Sangeeta
 

On Wed, 24 Jan 2007 09:45:02 +0100, Tsjerk Wassenaar wrote
> Hi Sangeeta,
> 
> To start with, you don't really describe a problem regarding pbc, as
> you've stated in the subject. Please make the subject reflect your
> problem or question directly. This will make it easier on the 
> repliers on this list to check whether they can be of any help. Most 
> of us read/discard messages based on the subject.
> 
> Now, you have three questions, which you've stated before, but
> apparently the answers were not informative enough. To start with the
> pbc, gromacs uses pbc unless explicitly stated otherwise, by adding
> pbc=no in the .mdp file.
> 
> Regarding the chlorides, I think you caught that you have to have an
> #include statement in the .top file, reading #include "ions.itp". The
> next thing to make sure is that the name you've used for your 
> chloride ions in the .top file matches those in the file ions.itp 
> listed for the force field you are using. It may be CL, Cl, Cl-. You 
> can try either or you can check the file ions.itp in your 
> $GMXDIR/share/gromacs/top directory.
> 
> Finally, regarding dssp, please explain what you tried to do, i.e.
> which command you've issued. Note that the file you mentioned is
> merely a temporary file.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On 1/24/07, sangeeta <sangeeta at bic.boseinst.ernet.in> wrote:
> >
> > Dear GROMACS list members,
> >
> >
> >    I have three questions,
> >
> >    My protein has +2 charge, so I added two Cl atoms through the program
> > genion and subsequently edited the  topol.top file, in spite of that 
while
> > running mdrun it gave an error that  "FATAL error, CL atom type can not 
be
> > found",I can not understand the problem.
> >    I wanted to include PBC in my simulation, I want to know that does
> > Gromacs by default use the option by minimum image convention or we have 
to
> > edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is
> > being included in my simulation?
> >     In spite of having dssp and running it I can not get the .xpm files.
> > Instead while dssp is going on some kind of files namely ddEZ117f 
ddOWnvlx
> > are being produced.How can I generate those xpm files?
> >     Waiting for your reply.
> >
> > regards
> > SANGEETA
> >
> > --
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> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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