[gmx-users] grompp error

[Nilesh Dhumal]

Thanks Justin,

Here I pasted water.top

;
;       File 'water.top' was generated
;       By user: ndhumal (36026)
;       On host: c63
;       At date: Thu Apr 21 14:52:38 2011
;
;       This is your topology file
;       Protein
;
; Include forcefield parameters
#include "ffoplsaa.itp"

; Include water topology
;#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
;#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
SOL               256

Nilesh

On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote:
>

>
> 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
>>
>>
>>
>>
>>
>
> --
> ========================================
>
>
> 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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