Dear Dr. Cheatam,
I have applid your suggestions and now I get
reasonable results.
The angle cutoff used was one of the mail problem(-1).
I have another question.
I have used the imaged trajectory file to save a
trajectory of closest 200 waters with noimage option.
When I viewed the trajectory in VMD the rna molecule
is rotating with some spead in random directions. I
have tried to get the trajectory with the original
unimaged trajectory without noimage option, But in the
obtained trajectory have waters spanning the entire
box.
(the number of water is reduced). I think it is a
problem with my input, P
Both my input files are attached.
Thanks in advance
Mathew
--- Thomas Cheatham <cheatham.chpc.utah.edu> wrote:
>
> > When series option is given the program
> continuously
> > gives an error message
> >
> > Set 1 ..WARNING in ptraj(), hbond: Too many
> > solvent acceptors near donor atom 17! (set
> > solventneighor higher)
>
> Right, what is happening is that for your given
> donor (atom 17) there are
> more solvent acceptors found than the program can
> handle and the comment
> says, increase solventneighbor (which is an option
> to the hbond command).
>
> If you increase solventneighbor, you can avoid this
> error...
>
> > I set the solventneighbor 15. then also the same
> error
> > message is obtained.
>
> If the same error message is obtained, it means that
> more than 15 solvents
> are within range. You can either decrease the
> distance cutoff for hbond
> or increase solventneighbor even higher.
>
> > But when the series option is avoided, the program
> > executes without any error messages.
>
> This does not mean it is "correct". The series
> command is necessary to
> understand any time dependent averages,
>
> > I have tried to calculate the radial distribution
> > functions. The program executes without any error
> > messages and the output files are written out, but
> the
> > programexits with a line,
> > -------------------------
> > Segmentation fault.
> > -------------------------
>
> This is unfortunate.
>
> > How can I use the 3column data obtained from the
> > radial
>
> I would guess that it doesn't always segfault if you
> have the file to
> view. The three oolumns are spacing, RDF and its
> integration (occupancy).
> You can look at that xmgr file by simply ignoring
> the third column...
>
>
>
>
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/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
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Received on Sat Nov 19 2005 - 11:53:00 PST
