[gmx-users] grompp error

[Justin Lemkul]

On 10/22/12 8:46 PM, Nur Syafiqah Abdul Ghani wrote:
> Dear All,
>
> Right now i want to do another simulation which is water and co-solvent,HFIP.
> I get the small compound file from
> http://compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files
> I need to used the all atom one and the force field that i used is gromos96.
> Right now i'm done packing the HFIP and the water by using packmol and
> change all the pdb file into gro file.
> Therefore I want to minimize them by using the command like below:
>
> grompp -f em1.mdp -c mixture.gro -p topol.top -o minimize.tpr -v
>
> and the error that coming out is :
>
> Fatal error:
> Syntax error - File solvent.itp, line 1
> Last line read:
> '[ atoms ]'
> Invalid order for directive atoms
>
>
> So, I already checked the problem by gedit the solvent.itp.Here is my itp file :
>

The first part of an .itp file needs to be a [moleculetype] directive that names 
the molecule and defines its number of exclusions.

> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
>      1   CH0    1    hfi     C1    1    0.384  12.0110
>      2     F    1    hfi     F1    1   -0.128  18.9984
>      3     F    1    hfi     F2    1   -0.128  18.9984
>      4     F    1    hfi     F3    1   -0.128  18.9984      ;  0.000
> .............
>      9   CH0    1    hfi     C3    3    0.384  12.0110
>     10     F    1    hfi     F4    3   -0.128  18.9984
>   ..........
> ; total charge of the molecule:   0.000
>
> [ bonds ]
> ;  ai   aj  funct   c0         c1
>      1    2    2   0.1360   7.2300e+06
>      1    3    2   0.1360   4.7700e+06
>    ...........
>      9   11    2   0.1360   4.7700e+06
>      9   12    2   0.1360   7.2300e+06
>
> [ pairs ]
> ;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
>      1    8    1
>      1   10    1
>      1   11    1
>      1   12    1
>      2    6    1
> .......
>      6    8    1
>      6   10    1
>      6   11    1
> .......
>      7   11    1
>      7   12    1
>      8    9    1
>
> [ angles ]
> ;  ai   aj   ak  funct   angle     fc
>      2    1    3    2    107.60   507.00
>      2    1    4    2    107.60   507.00
>      2    1    5    2    111.40   532.00
>      3    1    4    2    107.60   507.00
>    ......
>      5    9   10    2    111.40   532.00
>      5    9   11    2    111.40   532.00
>      5    9   12    2    109.50   618.00
>    ..........
>     11    9   12    2    107.60   507.00
>
> [ dihedrals ]
> ; GROMOS improper dihedrals
> ;  ai   aj   ak   al  funct   angle     fc
>
> [ dihedrals ]
> ;  ai   aj   ak   al  funct    ph0      cp     mult
>      2    1    5    9    1      0.00     3.77    3
>     ........
>
> [ exclusions ]
> ;  ai   aj  funct  ;  GROMOS 1-4 exclusions
>
> and the topology file is :
>

The first thing you need to #include is the parent force field, from which 
bonded and nonbonded parameters are taken.

-Justin

> ; Include topology for solvent
> #include "solvent.itp"
> ;
> ; Include water topology
> #include "gromos53a6.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
> ;
> [ system ]
> ; Name
> solvent in water box
> ;
> ;
> [ molecules ]
> ; Compound      #mols
> hfi                     .......
>
>
> Is thereany typing error that i seem cant see?
> I already compare with other problem but seems that I'm lost.
>
> Thanks in advance,
>
> Best Regards,
>
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> 013-7188131
> alternative email : syafiqahabdulghani at gmail.com
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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