Dear Dr.Cheatham,
Thank you very much for your reply.
I am using the ptraj version distributed with AMBER 8.
The series option to is not specified with the hbond
command.
When series option is given the program continuously
gives an error message
--------------------------------------------------------------------------
Processing AMBER trajectory file ../ade1l_md9.mdcrd
Set 1 ..WARNING in ptraj(), hbond: Too many
solvent acceptors near donor atom 17! (set
solventneighor higher)
....WARNING in ptraj(), hbond: Too many solvent
acceptors near donor atom 14! (set solventneighor
higher)
..WARNING in ptraj(), hbond: Too many solvent acceptors
near donor atom 14! (set solventneighor higher)
WARNING in ptraj(), hbond: Too many solvent acceptors
near donor atom 375! (set solventneighor higher)
..............
---------------------------------------------------------------------------
I set the solventneighbor 15. then also the same error
message is obtained.
But when the series option is avoided, the program
executes without any error messages.
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.
-------------------------
I have calcuated the backbone angles and sugar puckers
using ptraj erlier without any problem.
Is there any problem with my build?
Should I try to reinstall the program?
How can I use the 3column data obtained from the
radial
command in xmgr?
Thanking you,
Mathew
--- Thomas Cheatham <cheatham.chpc.utah.edu> wrote:
>
> > I have used ptraj to do some hbond analysis of an
> MD trajectory.
> > I have some doubts about the results. The
> %occupied is greater than
> > 1000 in many cases of solvent acceptor and solvent
> donor when the imaged
> > trajectory is used.
> > When the original trajectory is used the
> %occupied is around 700 in
> > many cases.
> > From the mail archive I understand that it means
> about 10 / 7 water
> > molecules are hydrogen bonded to the particular
> atom.
> > Is it normal?
> > Which one is the correct method? The output
> obtained is attached.
>
> At present the hbond facility does not image the
> distances, so it makes
> sense that after imaging the occupancies are higher.
> (since waters that
> were in adjacent periodic cells get imaged back). I
> will fix hbond to do
> imaging in the future.
>
> The next question is whether occupancies of > 100%
> up to 700-1000% are
> reasonable. If ptraj is working correctly, this
> would mean that there are
> between 7-10 waters interacting with the group
> (subject to no angle but a
> 3.5 A distance criteria). This seems high.
>
> To verify, you could try calculating a radial
> distribution function around
> the given groups to see if this many waters are
> within range.
>
> You could be including waters within the second
> water shell using a 3.5 A
> criteria (rather than say 3.2 A).
>
> Since your hbond command uses the default parameter
> for solventneighbors
> (i.e. 6) I find it problematic that 7-10 waters are
> found since a max of 6
> would be tracked. Therefore this looks like a bug.
>
> did you redefine solvent? This appears to be an old
> version of ptraj
> since the maxocc column was not specified.
>
> What version of ptraj are you using?
>
> I'd be happy to help you try to track this down...
>
> -- tec3.utah.edu
>
> \-/ Thomas E. Cheatham, III (Assistant Professor)
> College of Pharmacy
> -/- Departments of Med. Chem. and of
> Pharmaceutics and Pharm. Chem.
> /-\ Adjunct Asst Prof of Bioeng.; Center for High
> Performance Computing
> \-/ University of Utah, 30 S 2000 E, SH 201, Salt
> Lake City, UT 84112
> -/-
> /-\ tec3.utah.edu (801) 587-9652; FAX:
> (801) 585-9119
> \-/ BPRP295A
> http://www.chpc.utah.edu/~cheatham
>
>
>
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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 Fri Nov 18 2005 - 04:53:00 PST
