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
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