[gmx-users] grompp error

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> I am trying to run a simulation for flexiable water. I use the parameters
> from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file.
> 
> ; Derived from parsing of runfiles/alat.top.orig
>  [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> ;1               3               yes             0.5     0.5
> ; comb-rule 3 is square-root sigma, the OPLSAA version
> 
>  [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>  opls_116   OW  8      9.95140    -0.820       A    3.165492e-01 
> 6.50299455e-01
>  opls_117   HW  1      4.03200     0.410       A    0.00000e+00  0.00000e+00
> 
> [ bondtypes ]
> ; i    j  func       b0          kb
>  OW    HW      1    1.012   443153.3808  ; J. Chem. Phys. (2006),124,024503
> 
> 
> [ angletypes ]
> ;  i    j    k  func       th0       cth
>   HW     OW     HW      1   113.24    317.5656  ; J. Chem. Phys.
> (2006),124,024503
> 
> 
> I am geting the error for
> 
>  grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr
> 
> 
>  error I am getting
> 
> rogram grompp, VERSION 4.0.7
> Source code file: topio.c, line: 415
> 
> Fatal error:
> Syntax error - File water.top, line 26
> Last line read:
> '[ system ]'
> Invalid order for directive system
> 
>  How can I fix this error?
> 

Assemble the components of your .top in the correct order, as described in 
chapter 5 of the manual.  Without seeing the contents of "water.top" that's the 
best anyone can offer.

-Justin

> Nilesh
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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