[gmx-users] KALP-15 tutorial

[Justin Lemkul]

On 8/28/16 11:13 AM, Roshan Shrestha wrote:
> 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 ?
>

Your topology is out of order with respect to the coordinates.  Follow the 
tutorial exactly; it lays out what modifications to make.  Also note that "126s" 
is invalid and should just be the number 126.

The difference in system.gro and system_inflated.gro is that water has been 
deleted by InflateGRO.  It is supposed to do this.  Do not add any water to the 
system until it is done being packed, as instructed by the tutorial.

-Justin

>
>
>
> 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
>>
>>
>>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================