Hi all,<br><br>I have a few probIems/confusions and will be extremely thankful for any help. I added some "Cl- ions" by replacing water using "genion (and -nn)". It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I try to run grompp, it gives an error saying "no such molecule type Cl". So my questions are:<br>
1) How to avoid that error? Do I have to define a Cl.itp and add molecule type etc. ?<br>2) If I try to add Cl using -neutral option (as my system before already had a net +ve charge), it says "No ions to add and no potentials to calculate", why?<br>
3) Why is Cl listed in molecules and not [atoms] section?<br>4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else I would have to do?<br>
5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald geom=3dc, other than using walls option(I have my own channel walls in the system, so want to avoid them). Is there a way to use periodicity=xyz with coulumb-type=PME and ewald geom=3dc?<br>
<br>Thanks,<br>Manik<br clear="all"><br>-- <br>_________________<br>HAPAX LEGOMENA<br>