[gmx-users] Inflategro

ram bio rmbio861 at gmail.com
Thu Sep 17 16:42:22 CEST 2009 

Dear Gromacs Users,

While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have
some queries regarding the INFLATEGRO, Please have patience to read and
answer my queries:

1)  does the system.gro  should include the position restrained file of
KALP_newbox.gro after running genrestr, as i combined the ouput of genestr
to dppc128.gro to generate system.gro.

2) should both the box vectors in system.gro to be deleted or just the ones
under KALP structure, the other being at the end of the file.

3)then I updated the system.gro file to 17503 atoms from 138 atoms and
executed this command: perl INFLATEGRO  system.gro 4  DPP  14
inflated_system.gro 5 areaperlipid.dat

the output was as under:
Reading.....
Scaling lipids....
There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein....
Checking for overlap....
...this might actually take a while....
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 26    40
Protein Y-min/max: 25    39
X-range: 14 A    Y-range: 14 A
Building 14 X 14 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 2 nm^2
Area per lipid: 10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.4755772444444 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...
Done!

then, i updated the topol_dppc_top to 126 lipids

; System specifications
[ system ]
126-Lipid DPPC Bilayer

[ molecules ]
; molecule name nr.
DPPC 126
SOL 3655

and also updated the number of atoms in system.gro to 17403 and added 126
DPPC and 3655 SOL to topol.top file and executed the grompp command for
minimization as under:

grompp -f minim.mdp -c system.gro -p topol.top -o em.tpr

minim.mdp parameters are as under:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform
define          = -DSTRONG_POSRES
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and long
range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist        = 1.2        ; Cut-off for making neighbor list (short range
forces)
coulombtype    = PME        ; Treatment of long range electrostatic
interactions
rcoulomb    = 1.2        ; Short-range electrostatic cut-off
rvdw        = 1.2        ; Short-range Van der Waals cut-off
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)

the ouput of grompp was :

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 813 of the 2346 non-bonded parameter combinations

ERROR 1 [file topol.top, line 535]:
  No default G96Angle types

Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 904]:
  System has non-zero total charge: 4.000011e+00



processing coordinates...

WARNING 1 [file topol.top, line 904]:
  Bad box in file system.gro

Generated a cubic box    6.612 x    6.639 x    6.741
Warning: atom name 6439 in topol.top and system.gro does not match (OW - C1)
Warning: atom name 6440 in topol.top and system.gro does not match (HW1 -
C2)
Warning: atom name 6441 in topol.top and system.gro does not match (HW2 -
C3)
Warning: atom name 6442 in topol.top and system.gro does not match (OW - N4)
Warning: atom name 6443 in topol.top and system.gro does not match (HW1 -
C5)
Warning: atom name 6444 in topol.top and system.gro does not match (HW2 -
C6)
Warning: atom name 6445 in topol.top and system.gro does not match (OW - O7)
Warning: atom name 6446 in topol.top and system.gro does not match (HW1 -
P8)
Warning: atom name 6447 in topol.top and system.gro does not match (HW2 -
O9)
Warning: atom name 6448 in topol.top and system.gro does not match (OW -
O10)
Warning: atom name 6449 in topol.top and system.gro does not match (HW1 -
O11)
Warning: atom name 6450 in topol.top and system.gro does not match (HW2 -
C12)
Warning: atom name 6451 in topol.top and system.gro does not match (OW -
C13)
Warning: atom name 6452 in topol.top and system.gro does not match (HW1 -
O14)
Warning: atom name 6453 in topol.top and system.gro does not match (HW2 -
C15)
Warning: atom name 6454 in topol.top and system.gro does not match (OW -
O16)
Warning: atom name 6455 in topol.top and system.gro does not match (HW1 -
C17)
Warning: atom name 6456 in topol.top and system.gro does not match (HW2 -
C18)
Warning: atom name 6457 in topol.top and system.gro does not match (OW -
C19)
Warning: atom name 6458 in topol.top and system.gro does not match (HW1 -
C20)
(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 904]:
  10965 non-matching atom names
  atom names from topol.top will be used
  atom names from system.gro will be ignored


double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

There were 2 warnings

-------------------------------------------------------
Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 986

Fatal error:
There was 1 error in input file(s)
-------------------------------------------------------

then I executed mdrun -v -deffnm em

the output is :

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot= -3.06213e+05 Fmax= 5.37269e+03, atom=
3275
Step=    1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax= 2.40667e+03, atom=
3024
Step=    3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05 Fmax= 2.89119e+03, atom=
4225
Step=    5, Dmax= 3.6e-03 nm, Epot= -3.12590e+05 Fmax= 1.46759e+03, atom=
1365
Step=    6, Dmax= 4.3e-03 nm, Epot= -3.13033e+05 Fmax= 3.84000e+03, atom=
1365
Step=    7, Dmax= 5.2e-03 nm, Epot= -3.13600e+05 Fmax= 2.88681e+03, atom=
1365
Step=    8, Dmax= 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93217e+03, atom=
1365
Step=    9, Dmax= 7.5e-03 nm, Epot= -3.14102e+05 Fmax= 4.72470e+03, atom=
1365
Step=   11, Dmax= 4.5e-03 nm, Epot= -3.14801e+05 Fmax= 9.91096e+02, atom=
1365

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 12 steps
Potential Energy  = -3.1480106e+05
Maximum force     =  9.9109589e+02 on atom 1365
Norm of force     =  1.2181871e+02

so, as the minimization was occuring i started compressing the box using
this command : perl INFLATEGRO  system.gro 0.95  DPP 0  inflated_system.gro
5 areaperlipid.dat

the ouput was as follows:
Reading.....
Scaling lipids....
There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein....
Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 26    40
Protein Y-min/max: 25    39
X-range: 14 A    Y-range: 14 A
Building 14 X 14 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 2 nm^2
Area per lipid: 0.551947761890625 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 0.555854011890625 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 0.551947761890625 nm^2

Writing Area per lipid...
Done!

finally i repeated the mdrun -v -deffnm em and perl INFLATEGRO  system.gro
0.95  DPP 0  inflated_system.gro 5 areaperlipid.dat 27 times but there was
no change in the area per lipid values.

Could any body help me whether I am following the tutorial correctly, and if
not please correct me by your suggestions

Ram
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