[gmx-users] grompp error

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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"
> 

Up to this point, you haven't defined any molecules.  You've commented out every 
topology and applied a [position_restraints] directive to a non-existent 
moleculetype.  So you've defined a force field, and then a system for which no 
molecules exist, hence the error.

-Justin

> [ 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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>>
> 
> 
> 

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

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

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