Hi There,<br> I am running a psition restraint mdrun. <br>For the same I am selecting the part of the molecule surrounding my LIG, and restraining the rest of system for mdrun (using genpr)..<br>As my system is protein in water, it is not allowing me to select a part of SOL for position restraint and rest of SOL allowed for movement, while doing so it gave me error like....<br>
<br>-------------------------------------------------------<br>Program grompp_d, VERSION 3.3.3<br>Source code file: toppush.c, line: 1193<br><br>Fatal error:<br>[ file "posre.itp", line 1986 ]:<br>Atom index (2722) in position_restraints out of bounds (1-2626).<br>
This probably means that you have inserted topology section "position_restraints"<br>in a part belonging to a different molecule than you intended to.<br>In that case move the "position_restraints" section to the right molecule.<br>
-------------------------------------------------------<br> where 2722 is the first SOL entry in the .gro file.<br><br>And when I tried with keeping the whole water molecule moving (only the part of protein is kept on position restraint). iT runs successfully.<br>
Can somebody give an insight into the problem, or Is it not possible to divide SOL molecules <br>for keeping a part of SOl for position restraint...<br>I hope, I have clarified the question well.....if not please ask me further.<br>
<br>Looking for suggestions..<br><br>With Thanks,<br>Vivek<br><br>