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Dear Justin and all..<div><br></div><div>I have been struggled for the pass few weeks...</div><div>I follow the KALP-15 in DPPC tutorials but I am using my own protein instead.</div><div><br></div><div>I had successfully reached the step INFLATEGRO where 2 lipid removed from the upper layer n 2 lipids removed from the lower layer. Then i updated my topology with deducted 4 number of molecule of lipid.</div><div><br></div><div>then I generated the strong_porse.itp using the following command:</div><div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="font-family: courier; font-size: small; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000</span></div><div><span class="Apple-style-span" style="font-family: courier; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; font-size: 10pt; "><br></span></div><div><span class="Apple-style-span" style="font-family: courier; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; font-size: 10pt; ">here is how the strong_posre.itp file look like</span></div><div><span class="Apple-style-span" style="font-family: courier; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; font-size: 10pt; "><div>[ position_restraints ]</div><div>; i funct fcx fcy fcz</div><div> 1 1 100000 100000 100000</div><div> 2 1 100000 100000 100000</div><div> 3 1 100000 100000 100000</div><div> 4 1 100000 100000 100000</div><div> 5 1 100000 100000 100000</div></span></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;">.....</span></font></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;">....</span></font></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;">....</span></font></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;">...</span></font></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;"><div>3483 1 100000 100000 100000</div><div>3484 1 100000 100000 100000</div><div>3485 1 100000 100000 100000</div><div>3486 1 100000 100000 100000</div></span></font></div><div><font class="Apple-style-span" face="courier"><span class="Apple-style-span" style="-webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><br></span></font></div><div><span class="Apple-style-span" style="font-family: courier; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; font-size: 10pt; ">then i updated the topology (as shown below)</span></div><div><br></div><div><div>; Include Position restraint file</div><div>#ifdef POSRES</div><div>#include "posre.itp"</div><div>#endif</div><div><br></div><div>; Strong position restraints for InflateGRO</div><div>#ifdef STRONG_POSRES</div><div>#include "strong_posre.itp"</div><div>#endif</div><div><br></div><div>; Include DPPC chain topology</div><div>#include "dppc.itp"</div><div><br></div><div>; Include water topology</div><div>#include "spc.itp"</div><div><br></div><div>; System specifications</div><div>[ system ]</div><div>128-Lipid DPPC Bilayer </div><div><br></div><div>[ molecules ]</div><div>; molecule name nr.</div><div>DPP 124</div><div>SOL 3655</div><div><br></div><div><br></div><div><br></div><div><br></div><div>and I also add in the "define" line in the energyminimization.mdp file</div><div><br></div><div>here is my em.mdp file </div><div><br></div><div><div>define =-DSTRONG_POSRES</div><div>integrator = steep</div><div>nsteps = 200</div><div>constraints = none</div><div>emtol = 1000.0</div><div>nstcgsteep = 10 ; do a steep every 10 steps of cg</div><div>emstep = 0.01 ; used with steep</div><div>nstcomm = 1</div><div>coulombtype = PME</div><div>ns_type = grid</div><div>rlist = 1.0</div><div>rcoulomb = 1.0</div><div>rvdw = 1.4</div><div>Tcoupl = no</div><div>Pcoupl = no</div><div>gen_vel = no</div><div>nstxout = 0 ; write coords every # step</div><div>optimize_fft = yes</div><div><br></div><div><br></div><div>HOWEVER, I get this error when I proceed to the grompp step.</div><div><br></div><div><div>Fatal error:</div><div>Syntax error - File strong_posre.itp, line 3</div><div>Last line read:</div><div>'[ position_restraints ]'</div><div>Invalid order for directive position_restraints</div><div><br></div><div>Can anyone guide me in this?</div><div>Yr comments and advices are appreciated.</div><div><br></div><div>best regards</div><div><br></div></div></div><div>edmund</div></div> <br /><hr />Your E-mail and More On-the-Go. 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