[gmx-users] lipid restrain

[RINU KHATTRI]

hello everyone
its working simply add D flag in .itp file
but got anothe error in equilibrium2

gmx mdrun -nt X -deffnm npt

i used this command

and getting Expected an integer argument for option -nt

kindly help




On Sat, Jul 26, 2014 at 12:15 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello every one
> i am working on complex with POPC membrane i want to use position restrain
> in lipid but it is not working it's give error
>  file lipid_posre.itp, line 57 ]:
> Atom index (53) in position_restraints out of bounds (1-52).
> this probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> last line sof my topology file is
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "epi.itp"
>
> ; Include Position restraint file for UNK
> #ifdef DPOSRES_UNK
> #include "posre_unk.itp"
> #endif
>
> ; Include POPC side chain topology
> #include "popc.itp"
>
> ; Include Position restraint file for lipid
> #ifdef DPOSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> [moleculetype]
> POPC
> #ifdef DPOSRES_LIPID
> [ position_restraints ]
> ; i  funct  fcx    fcy    fcz
>    8    1    1000000   1000000   100000   ; restrains to a point x,y,z
>
> #endif
>
> ; Include topology for ions
> #include "gromos43a1_lipid.ff/ions.itp"
>
> [ system ]
> ; Name
> Displayed atoms in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> UNK    1
> POPC    122
> SOL    9410
> CL    15
> my min.mdp is
> define        = -DPOSRES_LIPID -DPOSRES -DPOSRES_UNK   ;position restrain
> on protein  ligand and POPC
>