<div style="font-family: 'Times New Roman'; font-size: 16px;"><br /><br /><span>On 01/20/10, <b class="name">Carla Jamous </b> <carlajamous@gmail.com> wrote:</span><blockquote cite="mid:e02c90f11001190756p4c44d987i463ef00d9077dde8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi,<br />I'm encountering a problem with pdb2gmx & occupancy. I searched the mailing list & followed this advice: "do NOT throw away crystallographic water molecules before you run genbox". </div></blockquote>Without context, that sounds like bad advice. Water molecules in active sites or some such are reasonable to wish to preserve. Bulk solvent will not usually matter. When quoting from the archive, please provide a URL, so that readers can get the context.<br _moz_dirty="" /><br _moz_dirty="" />Mark<br /><blockquote cite="mid:e02c90f11001190756p4c44d987i463ef00d9077dde8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">I kept my pdb's water mlolecules & ran pdb2gmx.<br />
<br />But still I get this warning:<br />" there were 0 atoms with zero occupancy and 1 atoms with occupancy unequal to one (out of 2658 atoms). Check your pdb file."<br /><br />What can I do to stop having this warning?<br />
<br />Thanks<br /><br />Carla<br />
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