AMBER Archive (2005)

Subject: AMBER: PTRAJ:"hbond" analysis

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Wed Mar 30 2005 - 11:15:30 CST

Dear All:

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

I have a protein with a Glutamic Acid near (Oxygen of an) Asparagine
residue. During a 1.2ns simulation, I imagined that perhaps water
molecule might bridge in a H-bond. So I specified OE1 oxygen of the
GLU residue as a DONOR; and H1 and H2 of WAT as potential ACCEPTORS:

***part of my script***:

trajin boxed6b_alltraj_centrdimg.coord

donor mask :63_at_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 \

This gave me a wat_hbond_63OE2.dat file WHICH I QUITE DON'T
UNDERSTAND. Please find it attached. My questions are:

(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?

(2) What does that last column mean :
|.-xxo**o |

means 8 symbols in these case, and in other cases only a few or
none.....

(3) What's the difference between "%occupied", "lifetime" and
"maxocc"....?

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

975 :63_at_OE2 | 33347 :9563_at_H2 33345 :9563_at_O | 45.83 2.699 (
0.11) 17.10 ( 8.78) 17.2 ( 13.0) 68 |.-xxo**o |

and
975 :63_at_OE2 | 33346 :9563_at_H1 33345 :9563_at_O | 18.83 2.718 (
0.12) 18.60 ( 9.00) 9.0 ( 3.5) 19 |x--.- . |

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.

(5) Reading the ultimate last row:
solvent donor | 5746 :363_at_H1 5745 :363_at_O | 156.83 2.695 (
0.12) 16.56 ( 9.18) 10.6 ( 11.0) 68 |@@@@@@@@@@|

Seems that WAT363 has so many @=>100% occupancy, why so? What then
about WAT9563....

May be it is rapidly exchanged....

Thanks in advance,
Cheers
Vineet

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