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From: Lorenzo Gontrani <l.gontrani.caspur.it>

Date: Fri, 16 Feb 2007 16:46:54 +0100

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.atom atom# :res.atom atom# :res.atom %occupied distance

angle lifetime maxocc

| 11 :1.O4 | 919 :292.H2 917 :292.O | 7.05 2.658 ( 0.11)

11.65 ( 4.95) 0.0 ( 0.2) 21 | --. |

| 11 :1.O4 | 505 :154.H2 503 :154.O | 6.49 2.660 ( 0.12)

11.16 ( 4.87) 0.0 ( 0.2) 12 | - - |

...............

...............

| 11 :1.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..

Date: Fri, 16 Feb 2007 16:46:54 +0100

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.atom atom# :res.atom atom# :res.atom %occupied distance

angle lifetime maxocc

| 11 :1.O4 | 919 :292.H2 917 :292.O | 7.05 2.658 ( 0.11)

11.65 ( 4.95) 0.0 ( 0.2) 21 | --. |

| 11 :1.O4 | 505 :154.H2 503 :154.O | 6.49 2.660 ( 0.12)

11.16 ( 4.87) 0.0 ( 0.2) 12 | - - |

...............

...............

| 11 :1.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 ======================================= ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun Feb 18 2007 - 06:07:32 PST

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