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<meta http-equiv="content-type" content="text/html; charset=utf-8">Dear all and Justin,<div> </div><div>I have try with the KALP-15 in DPPC tutorials..it was successfully done until Inflategro step.</div><div>then I tried with my own protein, I still having the same problems, while i wanna do the energy minimization after inflategro.</div><div><br></div><div>3 DPPC removed during inflategro...and i updated the number of molecules of DPPC lipid in topology..</div><div><br></div><div><br></div><div>here is how the strong_posre.itp file look like</div><div><div><br></div><div> [ position_restraints ]<br style="text-indent: 0in !important; "> ; i funct fcx fcy fcz<br style="text-indent: 0in !important; "> 1 1 100000 100000 100000<br style="text-indent: 0in !important; "> 2 1 100000 100000 100000<br style="text-indent: 0in !important; "> 3 1 100000 100000 100000<br style="text-indent: 0in !important; "> 4 1 100000 100000 100000<br style="text-indent: 0in !important; "> 5 1 100000 100000 100000<br style="text-indent: 0in !important; "> .....<br style="text-indent: 0in !important; "> ....<br style="text-indent: 0in !important; "> ....<br style="text-indent: 0in !important; ">3483 1 100000 100000 100000<br style="text-indent: 0in !important; ">3484 1 100000 100000 100000<br style="text-indent: 0in !important; ">3485 1 100000 100000 100000<br style="text-indent: 0in !important; ">3486 1 100000 100000 100000</div><div><br></div><div>ONLY protein included in the strong_posre.itp file....(this protein has 3486 atoms..)</div><div><br></div><div>then again i updated my topology...</div><div><br></div><div><br></div><div><div>; Include forcefield parameters</div><div>#include "ffG53a6_lipid.itp"</div><div><br></div><div><br></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 chain topologies</div><div>#include "topol_A.itp"</div><div>#include "topol_B.itp"</div><div><br></div><div>; Include water topology</div><div>#include "spc.itp"</div><div><br></div><div><br></div><div>#ifdef POSRES_WATER</div><div>; Position restraint for each water oxygen</div><div>[ position_restraints ]</div><div>; i funct fcx fcy fcz</div><div> 1 1 1000 1000 1000</div><div>#endif</div><div><br></div><div>; Include generic topology for ions</div><div>#include "ions.itp"</div><div><br></div><div>[ system ]</div><div>; Name</div><div>protein in dppc</div><div><br></div><div><br></div><div><br></div><div>[ molecules ]</div><div>; Compound #mols</div><div>Protein_A 1</div><div>Protein_B 1</div><div>DPPC 125</div></div><div><br></div><div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"> and I also add in the "define" line in the energyminimization.mdp file<br style="text-indent: 0in !important; "> <br style="text-indent: 0in !important; "> here is my em.mdp file <br style="text-indent: 0in !important; "> <br style="text-indent: 0in !important; "> define =-DSTRONG_POSRES<br style="text-indent: 0in !important; "> integrator = steep<br style="text-indent: 0in !important; "> nsteps = 200<br style="text-indent: 0in !important; "> constraints = none<br style="text-indent: 0in !important; "> emtol = 1000.0<br style="text-indent: 0in !important; "> nstcgsteep = 10 ; do a steep every 10 steps of cg<br style="text-indent: 0in !important; "> emstep = 0.01 ; used with steep<br style="text-indent: 0in !important; "> nstcomm = 1<br style="text-indent: 0in !important; "> coulombtype = PME<br style="text-indent: 0in !important; "> ns_type = grid<br style="text-indent: 0in !important; "> rlist = 1.0<br style="text-indent: 0in !important; "> rcoulomb = 1.0<br style="text-indent: 0in !important; "> rvdw = 1.4<br style="text-indent: 0in !important; "> Tcoupl = no<br style="text-indent: 0in !important; "> Pcoupl = no<br style="text-indent: 0in !important; "> gen_vel = no<br style="text-indent: 0in !important; "> nstxout = 0 ; write coords every # step<br style="text-indent: 0in !important; "> optimize_fft = yes<br style="text-indent: 0in !important; "> <br style="text-indent: 0in !important; "> <br style="text-indent: 0in !important; "> HOWEVER, I still get this error when I proceed to the grompp step.</div><div><br style="text-indent: 0in !important; "> <br style="text-indent: 0in !important; "> Fatal error:<br style="text-indent: 0in !important; ">Syntax error - File strong_posre.itp, line 3<br style="text-indent: 0in !important; "> Last line read:<br style="text-indent: 0in !important; "> '[ position_restraints ]'<br style="text-indent: 0in !important; "> Invalid order for directive position_restraints<br style="text-indent: 0in !important; "> </div><div><br></div><div>as Justin commented, only Protein is selected in strong posre, ( yea..i only selected the protein)</div><div><br style="text-indent: 0in !important; "> Can anyone guide me in this?<br style="text-indent: 0in !important; "> Yr comments and advices are appreciated.</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>edmund lee wrote:<br style="text-indent: 0in !important; ">> > Dear Justin and all..<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > I have been struggled for the pass few weeks...<br style="text-indent: 0in !important; ">> > I follow the KALP-15 in DPPC tutorials but I am using my own protein <br style="text-indent: 0in !important; ">> > instead.<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > I had successfully reached the step INFLATEGRO where 2 lipid removed <br style="text-indent: 0in !important; ">> > from the upper layer n 2 lipids removed from the lower layer. Then i <br style="text-indent: 0in !important; ">> > updated my topology with deducted 4 number of molecule of lipid.<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > then I generated the strong_porse.itp using the following command:<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > here is how the strong_posre.itp file look like<br style="text-indent: 0in !important; ">> > [ position_restraints ]<br style="text-indent: 0in !important; ">> > ; i funct fcx fcy fcz<br style="text-indent: 0in !important; ">> > 1 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 2 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 3 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 4 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 5 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > .....<br style="text-indent: 0in !important; ">> > ....<br style="text-indent: 0in !important; ">> > ....<br style="text-indent: 0in !important; ">> > ...<br style="text-indent: 0in !important; ">> > 3483 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 3484 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 3485 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > 3486 1 100000 100000 100000<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > then i updated the topology (as shown below)<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > ; Include Position restraint file<br style="text-indent: 0in !important; ">> > #ifdef POSRES<br style="text-indent: 0in !important; ">> > #include "posre.itp"<br style="text-indent: 0in !important; ">> > #endif<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > ; Strong position restraints for InflateGRO<br style="text-indent: 0in !important; ">> > #ifdef STRONG_POSRES<br style="text-indent: 0in !important; ">> > #include "strong_posre.itp"<br style="text-indent: 0in !important; ">> > #endif<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > ; Include DPPC chain topology<br style="text-indent: 0in !important; ">> > #include "dppc.itp"<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > ; Include water topology<br style="text-indent: 0in !important; ">> > #include "spc.itp"<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > ; System specifications<br style="text-indent: 0in !important; ">> > [ system ]<br style="text-indent: 0in !important; ">> > 128-Lipid DPPC Bilayer <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > [ molecules ]<br style="text-indent: 0in !important; ">> > ; molecule name nr.<br style="text-indent: 0in !important; ">> > DPP 124<br style="text-indent: 0in !important; ">> > SOL 3655<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > and I also add in the "define" line in the energyminimization.mdp file<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > here is my em.mdp file <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > define =-DSTRONG_POSRES<br style="text-indent: 0in !important; ">> > integrator = steep<br style="text-indent: 0in !important; ">> > nsteps = 200<br style="text-indent: 0in !important; ">> > constraints = none<br style="text-indent: 0in !important; ">> > emtol = 1000.0<br style="text-indent: 0in !important; ">> > nstcgsteep = 10 ; do a steep every 10 steps of cg<br style="text-indent: 0in !important; ">> > emstep = 0.01 ; used with steep<br style="text-indent: 0in !important; ">> > nstcomm = 1<br style="text-indent: 0in !important; ">> > coulombtype = PME<br style="text-indent: 0in !important; ">> > ns_type = grid<br style="text-indent: 0in !important; ">> > rlist = 1.0<br style="text-indent: 0in !important; ">> > rcoulomb = 1.0<br style="text-indent: 0in !important; ">> > rvdw = 1.4<br style="text-indent: 0in !important; ">> > Tcoupl = no<br style="text-indent: 0in !important; ">> > Pcoupl = no<br style="text-indent: 0in !important; ">> > gen_vel = no<br style="text-indent: 0in !important; ">> > nstxout = 0 ; write coords every # step<br style="text-indent: 0in !important; ">> > optimize_fft = yes<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > HOWEVER, I get this error when I proceed to the grompp step.<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > Fatal error:<br style="text-indent: 0in !important; ">> > Syntax error - File strong_posre.itp, line 3<br style="text-indent: 0in !important; ">> > Last line read:<br style="text-indent: 0in !important; ">> > '[ position_restraints ]'<br style="text-indent: 0in !important; ">> > Invalid order for directive position_restraints<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > Can anyone guide me in this?<br style="text-indent: 0in !important; ">> > Yr comments and advices are appreciated.<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> <br style="text-indent: 0in !important; ">> You have several problems:<br style="text-indent: 0in !important; ">> <br style="text-indent: 0in !important; ">> 1. Your [molecules] directive makes no reference to the protein that should be <br style="text-indent: 0in !important; ">> present.<br style="text-indent: 0in !important; ">> 2. Your "strong_posre.itp" file looks like it refers to the whole system; it <br style="text-indent: 0in !important; ">> should have been created from the protein only. You don't want to restrain <br style="text-indent: 0in !important; ">> everything in the system, anyway, and position restraints cannot be applied to a <br style="text-indent: 0in !important; ">> multiple molecule types in a single [position_restraints] directive.<br style="text-indent: 0in !important; ">> <br style="text-indent: 0in !important; ">> -Justin<br style="text-indent: 0in !important; ">> <br style="text-indent: 0in !important; ">> > best regards<br style="text-indent: 0in !important; ">> > <br style="text-indent: 0in !important; ">> > edmund<br style="text-indent: 0in !important; ">> > <div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div></div> <br /><hr />Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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