[gmx-users] Inflategro
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 17 16:50:21 CEST 2009
ram bio wrote:
> 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.
>
You don't include a position restraint file in a coordinate file :)
I give explicit instructions on what to do in section 2 of the following page:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> 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.
>
Just the ones in the KALP structure. Box vectors only ever belong on the very
last line of the .gro 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
>
Well, that's certainly wrong. There's a protein in there! As well, inflategro
deletes water molecules.
Follow closely the procedure I describe here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
Because it appears that your topology is incorrect even before the inflategro step.
> 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
>
The acetyl cap is problematic; for some reason pdb2gmx does not assign a value
for this angle. You can look it up in ffG53a6bon.itp
> 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'
>
Now this doesn't make sense with what you've shown above. Protein is recognized
in the topology, but that isn't true in the topology snippet from before.
Please provide accurate information, or else you won't be able to get any
reliable help!
> 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
>
This probably comes from the fact that you've deleted the wrong set of box vectors.
> 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
>
This is bad news. The topology is expecting water, but finding lipid. Probably
due to some inconsistency that I've mentioned above. Follow the instructions
carefully when setting up the topology. That's why I advise that it's one of
the most important (and detailed!) processes to go through.
>
> 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
>
Don't. If grompp is throwing that many errors, everything after this is
meaningless, especially if it thinks your lipids are water molecules. Never
plow ahead when faced with errors; it is a waste of time.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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