[gmx-users] protein in dppc

[Justin A. Lemkul]

edmund lee wrote:
> Dear Justin and all..
> 
> I have been struggled for the pass few weeks...
> I follow the KALP-15 in DPPC tutorials but I am using my own protein 
> instead.
> 
> I had successfully reached the step INFLATEGRO where 2 lipid removed 
> from the upper layer n 2 lipids removed from the lower layer. Then i 
> updated my topology with deducted 4 number of molecule of lipid.
> 
> then I generated the strong_porse.itp using the following command:
> 
> genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> 
> 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
> 
> then i updated the topology (as shown below)
> 
> ; 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 water topology
> #include "spc.itp"
> 
> ; System specifications
> [ system ]
> 128-Lipid DPPC Bilayer 
> 
> [ molecules ]
> ; molecule name nr.
> DPP            124
> SOL           3655
> 
> 
> 
> 
> 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 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
> 
> Can anyone guide me in this?
> Yr comments and advices are appreciated.
> 

You have several problems:

1. Your [molecules] directive makes no reference to the protein that should be 
present.
2. Your "strong_posre.itp" file looks like it refers to the whole system; it 
should have been created from the protein only.  You don't want to restrain 
everything in the system, anyway, and position restraints cannot be applied to a 
multiple molecule types in a single [position_restraints] directive.

-Justin

> best regards
> 
> edmund
> 
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-- 
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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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