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hmm, i thought smileys were not so cool... but thanks, i have my answer.<br>
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David wrote:
<blockquote cite="mid1103131397.4362.5.camel@h19n2fls34o1123.telia.com"
type="cite">
<pre wrap="">On Wed, 2004-12-15 at 16:44 +0000, Abil Aliev wrote:
</pre>
<blockquote type="cite">
<pre wrap="">thanks, David. what about 2 different types of tip4p:
"pdb2gmx -ff oplsaa -water tip4p" results in HO4 with HW1 for
crystallographic water, whereas "genbox -cs tip4p" gives MW1 for the
added water molecules (the other 3 atoms are the same). in fact, without
manually editing the gro file grompp simply fails, complaining about
different number of atoms in top and gro files.
</pre>
</blockquote>
<pre wrap=""><!---->Since you have discovered this, you can probably fix it too :).
Some MD equilibration will fix all your problems in this respect.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">with the above i get OW1,HW1,HW2 and HW4 for crystallogrphic waters
which are labelled as HO4. after editconf/genbox -cs tip4p i get a
different type for added water with HW1 above replaced by MW1. i can
change HW1 to MW1 and HO4 to HOH before genbox to get the grompp
working, but is this the right way to proceed?
</pre>
</blockquote>
<pre wrap="">
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</pre>
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