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<pre>"""</pre>
<pre>genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro
Have you done any basic tutorial material before diving head-first into this
more complicated topic?
The idea is this: pdb2gmx generates the topology for the protein. You can then
do whatever you choose with this definition of a protein. After pdb2gmx, you
also have a coordinate file that meets force field specifications as far as
protonation goes. This is the set of coordinates you should replicate, since it
is correct within the force field.<br>"""<br><br>I've done all the tutorial material hat is supplied with Gromacs...<br><br>I believe I may have got it. These are the steps I took.<br><br>pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro<br><br>vi polygly.top<br>Changed Protein count from 1 to 8<br><br>genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro<br><br>editconf -f polygly_8 -o -d 1.0<br><br>genbox -cp out -cs -p polygly -o b4em<br><br>grompp -v -f em -c b4em -o em -p polygly<br><br>mdrun -v -s em -o em -c after_em -g emlog<br><br>grompp -f pr -o pr -c after_em -r after_em -p polygly<br><br>mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &<br><br>grompp -v -f full -o full -c after_pr -p polygly<br><br>mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &<br><br>When I look at the simulation:<br><br>ngmx -s pr -full<br><br>There are 8 short peptides.<br><br>Does anything seem wrong with these steps?<br><br>Justin, thanks for the help :)<br><br></pre> </body>
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