Sir<br> i want to use makehole program (gromacs 3.1.4)and i used the grompp command on dmpc.pdb with position restraints as specified in the tutorial.<br> <br> the position restraint file is as follows :<br> [ position_restraints ]<br> ; atom type fx fy fz<br> 8 1 0.0 0.0 1000.0<br> <br> the tutorial says, this will restraint all phosphorous atoms in the bilayer in z-coordinates.<br> What does "type" specify? also, the pdb file has different number for every phosphorous atom of the dmpc molecules. Will specifying only '8' only , restraint all P8s? <br> <br> when i give the grompp command i get the following error:<br> .<br> .<br> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar<br> checking input for internal consistency...<br> calling /lib/cpp...<br>
cecmel311334_hole_dmpc.top:11:1: error: unterminated #else<br> cpp exit code: 256<br> Tried to execute: '/lib/cpp -I/usr/local/gromacs/share/top -DPOSRES cecmel311334_hole_dmpc.top > gromppZOiO4o'<br> The '/lib/cpp' command is defined in the .mdp file<br> processing topology...<br> Generated 1174 of the 2016 non-bonded parameter combinations<br> Cleaning up temporary file gromppZOiO4o<br> Fatal error: [ file "lipid_posre.itp", line 3 ]:<br> <span style="text-decoration: underline;">Atom index (8) in position_restraints out of bounds (1-3)<br> <br> </span>What does this mean? n please guide how to proceed..<br> <br> due regards<br> nur<br> <p> 
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