[gmx-users] Problems in gromacs

[karamyog singh]

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

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?

 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.

 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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