[gmx-users] KALP-15 tutorial

Sun Aug 28 17:13:54 CEST 2016

Actually, I thought that I made an error by minimizing system.gro instead
of system_inflated.gro. So, I ran energy minimization for
system_inflated.gro by renaming tutorial's minim.mdp as em.mdp-
gmx grompp -f em.mdp -c system_inflated.gro -p topol.top -o inflated_em1.tpr
But, I am again getting an error as-Warning: atom name 1 in topol.top and
system_inflated.gro does not match (C1 - CA)
Warning: atom name 2 in topol.top and system_inflated.gro does not match
(C2 - C)
Warning: atom name 3 in topol.top and system_inflated.gro does not match
(C3 - O)
Warning: atom name 4 in topol.top and system_inflated.gro does not match
(N4 - N)
Warning: atom name 5 in topol.top and system_inflated.gro does not match
(C5 - H)
Warning: atom name 6 in topol.top and system_inflated.gro does not match
(C6 - CA)
Warning: atom name 7 in topol.top and system_inflated.gro does not match
(O7 - C)
Warning: atom name 8 in topol.top and system_inflated.gro does not match
(P8 - O)
Warning: atom name 9 in topol.top and system_inflated.gro does not match
(O9 - N)
Warning: atom name 10 in topol.top and system_inflated.gro does not match
(O10 - H)
Warning: atom name 11 in topol.top and system_inflated.gro does not match
(O11 - CA)
Warning: atom name 12 in topol.top and system_inflated.gro does not match
(C12 - CB)
Warning: atom name 13 in topol.top and system_inflated.gro does not match
(C13 - CG)
Warning: atom name 14 in topol.top and system_inflated.gro does not match
(O14 - CD)
Warning: atom name 15 in topol.top and system_inflated.gro does not match
(C15 - CE)
Warning: atom name 16 in topol.top and system_inflated.gro does not match
(O16 - NZ)
Warning: atom name 17 in topol.top and system_inflated.gro does not match
(C17 - HZ1)
Warning: atom name 18 in topol.top and system_inflated.gro does not match
(C18 - HZ2)
Warning: atom name 19 in topol.top and system_inflated.gro does not match
(C19 - HZ3)
Warning: atom name 20 in topol.top and system_inflated.gro does not match
(C20 - C)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 930]:
  6438 non-matching atom names
  atom names from topol.top will be used
  atom names from system_inflated.gro will be ignored

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   126      Other residues
There are:    17    Protein residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 19311.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 216x216x56, spacing 0.119 0.119 0.118
Estimate for the relative computational load of the PME mesh part: 0.96

NOTE 4 [file em.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.

This run will generate roughly 1 Mb of data

There were 4 notes

There was 1 warning

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.3
Source code file:
/home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
line: 2107

Fatal error:
Too many warnings (1), gmx terminate
The end of my topol.top is-
 ; 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 "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
frame t= 1.000

[ molecules ]
; Compound        #mols
DPPC                126s
Protein             1

There are 17503 atoms in system.gro while only 6438 in system_inflated.gro.
Are the errors due to this difference ?

On Sun, Aug 28, 2016 at 3:34 PM, Roshan Shrestha <roshanpra at gmail.com>
wrote:

> After using this step-
> *perl inflategro.pl <http://inflategro.pl> system.gro 4 DPPC 14
> system_inflated.gro 5 area.dat*
> 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...
> Then I updated [ molecules] section of my topol.top as
> [ molecules ]
> ; Compound        #mols
> DPPC                126
> Protein             1
> Then I ran energy minimization. After that I used
> *perl inflategro.pl <http://inflategro.pl> EM.gro 0.95 DPPC 0
> system_shrink1.gro 5 area_shrink1.dat*
> I got,
> 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
>
> No protein coordinates found...
> Writing scaled bilayer & centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 10000    -9999
> Protein Y-min/max: 10000    -9999
> X-range: -19999 A    Y-range: -19999 A
> Building -19999 X -19999 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD..
> lower TMD..
> Area per protein: 0 nm^2
> Area per lipid: 0.583197761890625 nm^2
>
> Area per protein, upper half: 0 nm^2
> Area per lipid, upper leaflet : 0.583197761890625 nm^2
>
> Area per protein, lower half: 0 nm^2
> Area per lipid, lower leaflet : 0.583197761890625 nm^2
>
> Writing Area per lipid...
> Done!
>
> *Clearly there is some mistake in here as the Area per protein is 0 and
> area per lipid is very low compared to the experimental value.*
>
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
>
>
>

-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal