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Why CHARMM does not consider water as Hbond donor
#24306 05/13/10 10:42 PM
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I have run a script to count the number of Hbond between one glucose and the water. And it gave the result like:
Analysing hydrogen bond patterns for:
#donors #acceptors
1st sel: 5 6
2nd sel: 0 420


I wonder why water is not considered as a Hbond donor?

Re: Why CHARMM does not consider water as Hbond donor
mooctopus #24307 05/13/10 10:47 PM
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May I also ask what some of terms mean in Coor Hbond subcommands?
What is the difference between CUTHB and CUTHA?
What are IRHI DRH RHMAx ITHI DTH THMAx ?

Thanks a lot!


================================
COORdinates { HBONd } [CUTHB <real>] [CUTHA <real>] [IUNIt <int>] -
{ CONTact } [BRIDge <resnam>] [VERBose] [TCUT real] -
2X(atom-selection) traj-spec -
[IRHI <int> [DRH <real> ][RHMAx <real>] ] -
[ITHI <int> [DTH <real> ][THMAx <real>] ] -
[PBC [CUBIC|TO|RHDO BOXL|XSIZE <real> -
[YSIZE <real> [ZSIZE <real>] ] ]]

Re: Why CHARMM does not consider water as Hbond donor
mooctopus #24308 05/13/10 11:33 PM
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rmv Online Content
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Apparently the DONOR statements for TIP3 are not present in many of the topology files. You can add them in a script with the DONOR command (hbonds.doc). You can also fix the TIP3 definition in your topology file and make a new PSF.

There is more info on COOR HBOND toward the end of corman.doc which explains many of the keywords.


Rick Venable
computational chemist

Re: Why CHARMM does not consider water as Hbond donor
rmv #24311 05/14/10 07:42 PM
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The primary reason that TIP3 Hbond donors are not present in the standard RTFs is a concern about memory usage - this concern is probably not valid with modern computers (hint, hint).

The IRH and ITH keyword sets allow you to obtain histograms of hydrogen bond lengths and lifetimes.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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