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From: Vineet Pande <pande_vineet.hotmail.com>

Date: Thu, 31 Mar 2005 09:17:57 +0000

Dear Prof. Cheatham:

Thanks a lot for your detailed reply. I think now its much better to

understand for me whats going on.

Regards,

vineet

*>From: "Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>
*

*>Reply-To: amber.scripps.edu
*

*>To: amber.scripps.edu
*

*>Subject: Re: AMBER: PTRAJ:"hbond" analysis
*

*>Date: Wed, 30 Mar 2005 10:40:16 -0700 (Mountain Standard Time)
*

*>
*

*>
*

*> > I Used Ptraj for H-bond analysis. I have the following doubts >>>
*

*>
*

*>Doubts or results?
*

*>
*

*> > donor mask :63.OE2
*

*> > acceptor WAT O H1
*

*> > acceptor WAT O H2
*

*> >
*

*> > hbond series HBOND6B time 2 \
*

*> > out wat_hbond_63OE2.dat solventneighbor 5 \
*

*> > solventacceptor WAT O H1 solventacceptor WAT O H2 \
*

*>
*

*>OK, so you are looking at the interaction of *specific* waters (via the
*

*>acceptor command) and general (indistinguishable) waters with the
*

*>solventacceptor command.
*

*>
*

*> > (1) The distances look OK, but ALL the angles are too low. Since I
*

*> > used a cutoff of 120 deg (default), why these 20, 30, 40 etc.
*

*> > degrees are showing up?
*

*>
*

*>By default, the distance cutoff is 3.5 A and the angle is 120.0 degrees,
*

*>but this is an admittedly funny definition of the angle as I currently
*

*>look back at my code.
*

*>
*

*>The angle is calculated as the angle between the
*

*>
*

*> donor -- acceptorH -- acceptor
*

*>
*

*>If you had a linear h-bond, this angle would be 180.0. The angle cutoff
*

*>is, at 120.0, stating that the angle formed must be greater than 120.0.
*

*>
*

*>However, the angle *stored*, for some reason is 180.0 - angle, such that a
*

*>linear hbond would be zero degrees. Therefore, a value of ~30-40 is a
*

*>good hbond...
*

*>
*

*> > (2) What does that last column mean :
*

*> > |.-xxo**o |
*

*>
*

*>This is a schematic of occupancy as a function of time from the beginning
*

*>to the end of the trajectory; the darker the symbol (loosely), the greater
*

*>the occupancy; at the top of the .dat file you will see the definitions,
*

*>but basically for this case...
*

*>
*

*> |.-xxo**o |
*

*>
*

*>...you show partial occupancy at the beginning, getting larger and then
*

*>going away at the end of the trajectory (i.e. it is no longer formed).
*

*>
*

*> > (3) What's the difference between "%occupied", "lifetime" and
*

*> > "maxocc"....?
*

*> >
*

*> > (4) Reading the 1st and 5th rows:
*

*> >
*

*> | 45.83 2.699 (0.11) 17.10 ( 8.78) 17.2 ( 13.0) 68 |.-xxo**o
*

*>
*

*>%occupied is the percent of time the hbond is formed over the trajectory
*

*>(i.e. 45.83%). 2.699 and 17.10 are the distances and angles (along with
*

*>stddev in parenthesis). Lifetime is a measure of the average time the
*

*>hbond is formed, i.e. we sum up all the times from intervals where
*

*>hbond is present and divide by the number of intervals, so this basically
*

*>states that you average lifetime (or amount of time the h-bond was formed)
*

*>at 17.2 ps (assuming you set the time variable correctly). Max occupied
*

*>is the maximum number of (contiguous) frames (minus instantaneous gaps)
*

*>the h-bond was occupied; in your case this is 68 frames * 2 ps or 136 ps.
*

*>
*

*> > IS IT SAFE TO SAY that WAT9563 showed 68+19=87% maximum occupancy
*

*> > and 45.83+18.83=64.66% occupancy.....if its correct, then what's the
*

*> > difference between two options.
*

*>
*

*>Yes, according to your definition of a h-bond (i.e. 3.5 A cutoff and 120
*

*>degree angle criteria) the single water (interacting via H1 or H2) is
*

*>occupied 87% of the time.
*

*>
*

*> > (5) Reading the ultimate last row:
*

*> > solvent donor | 5746 :363.H1 5745 :363.O | 156.83 2.695 (
*

*> > 0.12) 16.56 ( 9.18) 10.6 ( 11.0) 68 |..........|
*

*>
*

*>This is more tricky and will depend your definition of solventdonor (which
*

*>was not in your script/command). Solventdonor provides a way to look at
*

*>the interaction of any of a list of waters or ions or what not with your
*

*>acceptor.
*

*>
*

*>If you assume that solventdonor above was WAT O, this states that a water
*

*>interacted with residue :363 156.8% of the time. How can this be? More
*

*>than a single water can satisfy the criteria; the maximum number that can
*

*>interact with a given donor/acceptor is given by the solventneighbor
*

*>value. If you blow this limit, the program will warn you.
*

*>
*

*>If you want more information, ad naseum, set prnlev 5 before running
*

*>hbond. It is a complicated bit of code but intends to be general.
*

*>
*

*>You could define solventdonor Na+ Na+ solventacceptor Na+ Na+ Na+ to look
*

*>at ion interaction with a residue (ignoring the angle cutoff since it
*

*>doesn't make sense), etc.
*

*>
*

*>Good luck.
*

*>
*

*>
*

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*

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*

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Received on Thu Mar 31 2005 - 10:53:00 PST

Date: Thu, 31 Mar 2005 09:17:57 +0000

Dear Prof. Cheatham:

Thanks a lot for your detailed reply. I think now its much better to

understand for me whats going on.

Regards,

vineet

_________________________________________________________________

Don't just search. Find. Check out the new MSN Search!

http://search.msn.com/

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Received on Thu Mar 31 2005 - 10:53:00 PST

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