From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 21 2011 - 06:55:18 CDT

You will probably find the Hydrogen Bonds plugin to be more intuitive. Look under Extensions -> Analysis.

On Oct 20, 2011, at 2:19 AM, subrata paul wrote:

> Dear VMD user
> I am simulating disscharide and water system in Amber.
> I want to calculate Hbond via VMD
> My atom selection for water- water hydrogen bond
> (I want to number of hydrogen bond per water molecule??)
>
> set selection_O [stomselect top "name O "]
> measure hbonds 3.4 45 $selection_O
> It gave
> {2943 2364 4782 3336 4014 2910 3483 3150 4566 3915 1467 1383 2397 1287 2778 2178 2136 4542 3885 3609 2718 1419 1359 1983 1506 4206 4968 1671 5229 3255 4776 1671 2067 2979 4497 4698 4626 3807 2997 3669 3162 1149 3243 3411 2307 3087 4050 4920 4425 3582 5013 1161 3021 1170 3501 4500 4500 3003 4878 3132 4323 3942 4434 4434 1527 2604 2409 2226 1590 1476 1749 4908 2709 4287 4677 4491 4440 3297 5292 4305 3705 1563 3966 4794 2613 1221 1776 4962 3618 2574 4809 5085 2343 2079 2391 1296 4398 4788 1869 3795 3741 2457 5295 1665 4917 4572 1488 4122 3201 2514 2958 3165 3744 3057 3918 4725 1806 1629 1500 4335 4065 4614 3111 2895 4056 4218 3840 2502 4929 3096 2463 4515 3837 5301 3015 4593 1743 3702 1908 2490} {1371 3381 4983 3276 4149 1692 1257 1572 3885 1467 3726 3372 3393 3927 1566 4722 3429 4722 3813 4632 2325 3183 2259 1605 1218 1581 4206 1416 4827 1662 3093 4551 3348 4497 5256 1779 3474 3474 1542 1449 3012 3312 4944 4938
>
> is this a correct command line and correct atom selection???
>
> what this number represent.
>
>
> thanking You
> Subrata Paul
>
> Dr Sandip Paul
> Dept of chemistry
> IIT guwahati.