Hi, If I am allowed to do some advertisement:
you could try the tool g_membed for inserting proteins as well http://wwwuser.gwdg.de/~ggroenh/membed.html Gerrit gmx-users-requ...@gromacs.org wrote: > 2. protein in dppc (edmund lee) > > Date: Tue, 23 Feb 2010 15:55:36 +0800 > From: edmund lee <eyemnoob2...@hotmail.com> > Subject: [gmx-users] protein in dppc > To: <gmx-users@gromacs.org> > Message-ID: <snt122-w306118246354907dd2561edd...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Dear Justin and all.. > I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC > tutorials but I am using my own protein instead. > 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. > then I generated the strong_porse.itp using the following command: > genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 > here is how the strong_posre.itp file look like[ position_restraints ]; i > funct fcx fcy fcz 1 1 100000 100000 > 100000 2 1 100000 100000 100000 3 1 100000 > 100000 100000 4 1 100000 100000 100000 5 1 > 100000 100000 100000................3483 1 100000 100000 > 1000003484 1 100000 100000 1000003485 1 100000 > 100000 1000003486 1 100000 100000 100000 > then i updated the topology (as shown below) > ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif > ; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include > "strong_posre.itp"#endif > ; Include DPPC chain topology#include "dppc.itp" > ; Include water topology#include "spc.itp" > ; System specifications[ system ]128-Lipid DPPC Bilayer > [ molecules ]; molecule name nr.DPP 124SOL 3655 > > > > and I also add in the "define" line in the energyminimization.mdp file > here is my em.mdp file > define =-DSTRONG_POSRESintegrator = steepnsteps > = 200constraints = noneemtol > = 1000.0nstcgsteep = 10 ; do a steep every 10 steps of cgemstep > = 0.01 ; used with steepnstcomm = 1coulombtype > = PMEns_type = gridrlist = 1.0rcoulomb > = 1.0rvdw = 1.4Tcoupl = > noPcoupl = nogen_vel = nonstxout > = 0 ; write coords every # stepoptimize_fft = yes > > HOWEVER, I get this error when I proceed to the grompp step. > Fatal error:Syntax error - File strong_posre.itp, line 3Last line read:'[ > position_restraints ]'Invalid order for directive position_restraints > Can anyone guide me in this?Yr comments and advices are appreciated. > best regards > edmund > _________________________________________________________________ > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
