<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
just to summarise, the following works:<br>
<br>
pdb2gmx -ff oplsaa -water tip4p -f sum.pdb -p speptide -o speptide<br>
vi speptide.gro<br>
:%s/ OW/MW1 ; OW and HW3 have the same xyz<br>
:%s/HW3/OW4<br>
:%s/HW2/HW3<br>
:%s/HW1/HW2<br>
:%s/HO4/SOL<br>
editconf, then<br>
genbox -cp out -cs tip4p.gro -o b4em -p speptide<br>
vi em.mdp<br>
define = -DPOSRES_WATER<br>
constraints = none<br>
integrator = steep<br>
nsteps = 100<br>
grompp, then mpirun c0-1 mdrun_d -v -s em -o em -c after_em -g emlog<br>
...<br>
Potential Energy = -193192<br>
Maximum force = 1676<br>
<br>
<br>
<blockquote cite="mid41C07D80.3050709@yahoo.co.uk" type="cite">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="">_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext"
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</pre>
</blockquote>
</blockquote>
<br>
<pre wrap="">
<hr size="4" width="90%">
</pre>
</blockquote>
<br>
<blockquote cite="mid41C07D80.3050709@yahoo.co.uk" type="cite">
<pre wrap="">_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.</pre>
</blockquote>
<br>
</body>
</html>