[gmx-users] mdrun_hole problem again

[alokjain at iitk.ac.in]

Dear All,
         two days back I posted a question regarding mdrun-hole but my
problem has still not ben solved,so I am writing it again in more
elaborate form. I appreciate any comment on my procedure.

In sort my problem is, I am not getting any output from modified
mdrun_hole program.

Here are the series of steps I follow.

1) First I took well equilibrated pope.pdb file from Dr. Peter tieleman site.

2) I align my protein with respect to pope bilayer by using editconf.

3)I used make_hole.pl script (comes with modified mdrun program..thanks to
Dr. Grahm smith) to make a hole,by following command

make_hole.pl -f inbilayer.pdb -o outbilayer.pdb -r 1.5 -lipat P8 -lipid POPE

it created the hole of my desired size.I  visualized the output pdb file,
it was visible.

4)I used GRASP and generated the molecular surface of my protein by the
procedure describe in the tutorial .

5) I used normal grompp and generated the run.tpr file.I used following
command

grompp -v -f run.mdp -po run_out -c outbilayer.pdb -r outbilayer.pdb -p
test.top -o run.tpr

my test.top file

############################# test.top ###############################
; topology for a pure POPE bilayer with 340 lipids and 6729 SPC water
; molecules

#include "/home/gromds/alok/membrane-protein/ffgmx.itp"
#include "/home/gromds/alok/membrane-protein/pope.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Pure POPE bilayer with 340 lipids and 6729 water molecules

[ molecules ]
; name  number
POPE    340
SOL     6729

######################################################################


my run.mdp file looks like it....

############################ run.mdp #################################

define                   = -DPOSRES_LIPID -DFLEX_SPC
integrator               = md
dt                       = 0.002
nsteps                   = 50000
nstxout                  = 50
nstvout                  = 50
nstlog                   = 5
nstenergy                = 25
nstxtcout                = 25
xtc_grps                 = POPE  SOL
energygrps               = POPE  SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 0.9
vdw-type                 = Cut-off
tcoupl                   = Berendsen
tc-grps                  = POPE  SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 10
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
####################################################################

6) Finally I tried to run modified mdrun_hole program.
It seems to run (I checked by top command), but it is not giving me any
output. It generated *.log (but no energy value, noe even for zeroth
time), *.edr (0kb) ...and no *.trr, *.xtc, *.gro files.

I am using following command.

mdrun_modified  -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -e
run.edr -g run.log -hole -holep for_hole.mdp

I checked validity of my run.tpr file by running it in normal mdrun
(3.1.4) it was running fine..

my for_hole.mdp files as follows.

###########################3## for_hole.mdp ############################
holetype                 = Grasp_ascii
hfm                      = 10
molsurf_file             = /home/gromds/alok/membrane-protein/out
sofs                     = 0
hp1                      = 1
hp2                      = 17680
supf                     = 10
resforces                = yes
molsurf_log              = /home/gromds/alok/membrane-protein/test.log
debugsurf                = yes
sfm                      = 10.0
s1                       = 17681
s2                       = 37867
hz                       = 3.0
hz1                      = 0
hz2                      = 6.0
#######################################################################

I tried with debugsurf = yes and no option but no success, even it does
not produce molsurfpdb.pdb & insidesurf.pdb file with yes option.

please suggest me somthing. I am stuck at this point.

Thanks a lot,
Alok