AMBER Archive (2007)

Subject: AMBER: H-bond ptraj dilemma

From: Lorenzo Gontrani (l.gontrani_at_caspur.it)
Date: Fri Feb 16 2007 - 09:46:54 CST

Dear all,
I would like some help to interpret the results of a MD simulation (8000
frames in total) of a molecule with several HB bond donors..
I used two methods:
1) ptraj routine "hbond" to calculate the "occupancy" of water around the HB
centers (distance cutoff 3.0, angular cutoff 160°)
2) ptraj "watershell" routine, giving H1 (or H2) water atoms as solvent (with
distance range 1.55-2.00 for the donor-H distance.

I cannot quantify the results I obtain for a center (which I know from
experiments to be the most hydrated).
I get in the first analysis:

        DONOR ACCEPTORH ACCEPTOR
  atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance
angle lifetime maxocc
| 11 :1_at_O4 | 919 :292_at_H2 917 :292_at_O | 7.05 2.658 ( 0.11)
11.65 ( 4.95) 0.0 ( 0.2) 21 | --. |
| 11 :1_at_O4 | 505 :154_at_H2 503 :154_at_O | 6.49 2.660 ( 0.12)
11.16 ( 4.87) 0.0 ( 0.2) 12 | - - |
...............
...............
| 11 :1_at_O4 | solvent acceptor | 139.60 2.665 ( 0.12)
11.45 ( 4.88) 0.0 ( 0.2) 27 |@@@@@@@@@@|

And, in the second case (elaborated from watershell output; H can be either H1
or H2 atom type)

O4

0 H
25/8000 (0,3125%)
1 H
1309/8000 (16,3625%)
2 H
6141/8000 (76,7625%)
3 H
525/8000 (6,5625%)

Of course, hbond result tells me that there is surely one water molecule, and
in some cases two molecules, since the occupancy is 139.60%..I cannot derive
a mathematical relation, since the "two" cases contain the "one" cases
Can I get the result frame by frame somehow (apart from using the
distance-only watershell command? Is there a way to get this information from
hbond routine (i.e. setting some "verbosity" parameter?

Thanks for any help you could give me

Regards

Lorenzo

I hope to have made myself understood.. 

-- 
=======================================

Lorenzo Gontrani

CASPUR - http://www.caspur.it
Consorzio per le Applicazioni di Supercalcolo Per Università e Ricerca
via dei Tizii, 6 - 00185 Roma
Tel +39 06 44486812 
Fax +39 06 4957083 
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it

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