[gmx-users] Inflategro
Pramod Akula
ab.pramod at gmail.com
Thu Sep 17 17:12:18 CEST 2009
Dear Justin,
Thanks for the suggestions.
will be back aftersome time as i am redoing it. Please check me for the
accuracy in steps in near future.
Ram
On Thu, Sep 17, 2009 at 8:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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