[gmx-users] Problems in gromacs

[David van der Spoel]

karamyog singh wrote:
> Greeting gromacs users. I am trying to use gromacs to simulate metals. I 
> am trying to simulate BCC Iron. But I get the following error message.
> 
> Fatal error: Invalid order for directive moleculetype, file 
> ""topol.top"", line 5

read chapter 5 in the manual about topology files.

> 
> I am sending you my input files. Please help me and tell me what is 
> wrong with my files. Also can you tell me if it is possible to simulate 
> metallic crystals using gromacs. Mostly people have worked on Bio 
> Molecules. However I believe that I should be able to simulate Metallic 
> structures if I modify the source codes a bit. Also, Can you please tell 
> me if I can use my own potential functions?
Depends on what you want. CHeck manual on tabulated functions.


> 
>  I downloaded force fields made by other people, I have modified them 
> too to include xb_1 bond type and FE FE interaction. These modifications 
> have been done in ffG53a6.rtp and ffG53a6bon.itp. These files are in 
> 53a6.tar.gz on the force field download section of the website 
> www.gromacs.org <http://www.gromacs.org>.
> 
>  I request you to please help me out as soon as you can. :)
> 
> 
> ------------------------------------------
> grompp.mdp
> 
> NES STARTING WITH ';' ARE COMMENTS
> title           = Minimization of Hen Egg White Lysozyme (1AKI.pdb)     
> ; Title of run
> 
> ; The following lines tell the program the standard locations where to 
> find certain files
> cpp             = /lib/cpp      ; Preprocessor
> include         = -I../top      ; Directories to include in the topology 
> format
> 
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent 
> minimization)
> emtol           = 1.0           ; Stop minimization when the maximum 
> force < 1.0 kJ/mol
> nsteps          = 200           ; Maximum number of (minimization) steps 
> to perform
> nstenergy       = 10            ; Write energies to disk every nstenergy 
> steps
> nstxtcout       = 10            ; Write coordinates to disk every 
> nstxtcout steps
> xtc_grps        = Protein       ; Which coordinate group(s) to write to disk
> energygrps      = Protein       ; Which energy group(s) to write to disk
> 
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist         = 5             ; Frequency to update the neighbor list 
> and long range forces
> ns_type         = simple        ; Method to determine neighbor list 
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list 
> (short range forces)
> coulombtype     = cut-off       ; Treatment of long range electrostatic 
> interactions
> rcoulomb        = 1.0           ; long range electrostatic cut-off
> rvdw            = 1.0           ; long range Van der Waals cut-off
> constraints     = none          ; Bond types to replace by constraints
> pbc             = yes           ; Periodic Boundary Conditions (yes/no)
> ----------------------------------------------
> topol.top
> #include "ffG53a6.itp"
> ;#include "ffgmx.rtp"
> ;#include "ffgmx.atp"
> 
> [ moleculetype ]
>  Ions   3
> 
> [ atoms ]
>      1          Fe      1    HEME     FE     1      0    55.870
>      2          Fe      2    HEME     FE     1      0    55.870
>      3          Fe      3    HEME     FE     1      0    55.870
>      4          Fe      4    HEME     FE     2      0    55.870
>      5          Fe      5    HEME     FE     2      0    55.870
>      6          Fe      6    HEME     FE     2      0    55.870
>      7          Fe      7    HEME     FE     2      0    55.870
>      8          Fe      8    HEME     FE     3      0    55.870
>      9          Fe      9    HEME     FE     3      0    55.870
> 
> [ bonds ]
> 
>  1 2 1 0.1000 1.7800e+7
> --------------------------------------------------
> Pure Fe
>  9
>   1Fe   FE    1  0.00 0.00 0.00  0.000 0.000 0.000
>   2Fe   FE    2  2.70 0.00 0.00  0.000 0.000 0.000
>   3Fe   FE    3  0.00 2.70 0.00  0.000 0.000 0.000
>   4Fe   FE    4  0.00 0.00 2.70  0.000 0.000 0.000
>   5Fe   FE    5  0.00 2.70 2.70  0.000 0.000 0.000
>   6Fe   FE    6  2.70 0.00 2.70  0.000 0.000 0.000
>   7Fe   FE    7  2.70 2.70 0.00  0.000 0.000 0.000
>   8Fe   FE    8  2.70 2.70 2.70  0.000 0.000 0.000
>   9Fe   FE    9  1.35 1.35 1.35  0.000 0.000 0.000
> 
> 
> conf.gro
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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