[gmx-users] protein in dppc

[Justin A. Lemkul]

edmund lee wrote:
> Dear all and Justin,
>  
> I have try with the KALP-15 in DPPC tutorials..it was successfully done 
> until Inflategro step.
> then I tried with my own protein, I still having the same problems, 
> while i wanna do the energy minimization after inflategro.
> 
> 3 DPPC removed during inflategro...and i updated the number of molecules 
> of DPPC lipid in topology..
> 
> 
> here is how the strong_posre.itp file look like
> 
>  [ position_restraints ]
>  ; i funct fcx fcy fcz
>  1 1 100000 100000 100000
>  2 1 100000 100000 100000
>  3 1 100000 100000 100000
>  4 1 100000 100000 100000
>  5 1 100000 100000 100000
>  .....
>  ....
>  ....
> 3483 1 100000 100000 100000
> 3484 1 100000 100000 100000
> 3485 1 100000 100000 100000
> 3486 1 100000 100000 100000
> 
> ONLY protein included in the strong_posre.itp file....(this protein has 
> 3486 atoms..)
> 
> then again i updated my topology...
> 
> 
> ; Include forcefield parameters
> #include "ffG53a6_lipid.itp"
> 
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
> 
> ; Include DPPC chain topology
> #include "dppc.itp"
> 
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.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 in dppc
> 
> 
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> DPPC               125
> 
> 
>  and I also add in the "define" line in the energyminimization.mdp file
>  
>  here is my em.mdp file 
>  
>  define =-DSTRONG_POSRES
>  integrator = steep
>  nsteps = 200
>  constraints = none
>  emtol = 1000.0
>  nstcgsteep = 10 ; do a steep every 10 steps of cg
>  emstep = 0.01 ; used with steep
>  nstcomm = 1
>  coulombtype = PME
>  ns_type = grid
>  rlist = 1.0
>  rcoulomb = 1.0
>  rvdw = 1.4
>  Tcoupl = no
>  Pcoupl = no
>  gen_vel = no
>  nstxout = 0 ; write coords every # step
>  optimize_fft = yes
>  
>  
>  HOWEVER, I still get this error when I proceed to the grompp step.
> 
>  
>  Fatal error:
> Syntax error - File strong_posre.itp, line 3
>  Last line read:
>  '[ position_restraints ]'
>  Invalid order for directive position_restraints
>  
> 
> as Justin commented, only Protein is selected in strong posre, ( yea..i 
> only selected the protein)
> 
>  Can anyone guide me in this?
>  Yr comments and advices are appreciated.
> 

As the error message indicates, your topology is completely out of order.  See 
the examples on the "Errors" page of the Gromacs wiki:

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults

Specifically, you are defining position restraints in the topology before you 
have defined any molecules, so grompp doesn't know what to do with them.  The 
examples of "WRONG" and "RIGHT" on the above page should illustrate this principle.

-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

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