I am using Ambertools 1.2 with all patched applied and this also happens to me.
BTW, the compilation of Ambertools 1.2 successfully ended with "Completed installation of AmberTools, version 1.1"
======= 2009-01-10 02:59:38 David A. Case wrote=======
>On Fri, Jan 09, 2009, Bill Ross wrote:
>
>> Not only does H3 change into 2H, but it makes for duplicate 2H atoms.
>
>I suspect the original poster has an old version of ambpdb -- this
>should have been fixed in AmberTools version 1.2.
>
>...dac
>
>
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Received on Sun Jan 11 2009 - 01:19:17 PST
