edmund lee wrote:
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 100000
3484 1 100000 100000 100000
3485 1 100000 100000 100000
3486 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 124
SOL 3655
and I also add in the "define" line in the energyminimization.mdp file
here is my em.mdp file
define =-DSTRONG_POSRES
integrator = steep
nsteps = 200
constraints = none
emtol = 1000.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
coulombtype = PME
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes
HOWEVER, I get this error when I proceed to the grompp step.
Fatal error:
Syntax error - File strong_posre.itp, line 3
Last line read:
'[ position_restraints ]'
Invalid order for directive position_restraints
Can anyone guide me in this?
Yr comments and advices are appreciated.
You have several problems:
1. Your [molecules] directive makes no reference to the protein that should be
present.
2. Your "strong_posre.itp" file looks like it refers to the whole system; it
should have been created from the protein only. You don't want to restrain
everything in the system, anyway, and position restraints cannot be applied to a
multiple molecule types in a single [position_restraints] directive.
-Justin
best regards
edmund
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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