[gmx-users] position restrain

[Justin A. Lemkul]

parto haghighi wrote:
> Dear GMX users,
> I am working on lipid_drg system
> my drug molecule has 23 atoms.
> 
> [ moleculetype ]
> ; Name nrexcl
> DRG      3
> 
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1  DRG     CAA     1   -0.073  15.0350
>      2       CH2     1  DRG     CAH     2    0.115  14.0270
>      3       CH2     1  DRG     CAI     3    0.367  14.0270
>      4        NL     1  DRG       N     4   -0.448  14.0067
>      5         H     1  DRG      H1     5    0.346   1.0080
>      6         H     1  DRG      H2     6    0.367   1.0080
>      7       CH1     1  DRG      CA     7    0.297  13.0190
>      8       CH3     1  DRG      CB     8    0.000  15.0350
>      9         C     1  DRG       C     9    0.743  12.0110
>     10         O     1  DRG       O    10   -0.598  15.9994
>     11         N     1  DRG     NAK    11   -0.776  14.0067
>     12         H     1  DRG     HAK    12    0.400  1.0080
>     13         C     1  DRG     CAP    13    0.470  12.0110
>     14       CR1     1  DRG     CAG    14    0.157  12.0110
>     15       CH3     1  DRG     CAL    15   -0.072   1.0080
>     16       CR1     1  DRG     CAF    16   -0.309  12.0110
>     17        HC     1  DRG     HB4    17    0.253  1.0080
>     18         S     1  DRG     SAM    18    0.089  32.0600
>     19         C     1  DRG     CAQ    19   -0.508  12.0110
>     20         C     1  DRG     CAN    20    0.968  12.0110
>     21         O     1  DRG     OAD    21   -0.619  15.9994
>     22        OA     1  DRG     OAL    22   -0.347  15.9994
>     23       CH3     1  DRG     CAB    23    0.178  15.0350
> 
> and I have added 12 drugs in bilayer + sol and ion:
> 
> [ molecules ]
> ; Compound        #mols
> DRG         12
> DMPC        128
> SOL         1943
> CL          12
> 
> At the NVT step:
> I have to use position restrain for 12 drug molecules which I have
> added in bilayer, so I applied genrestr to make drg_posres.itp
> 
> genrestr -f lip_12drg_solv_ion_em.gro -o drg_posre.itp -fc 1000 1000 1000
> 
> and I modified end of topology:
> 
> ; Include Position restraint file
> #ifdef POSRES_DRG
> #include "drg_posre.itp"
> #endif
> 
> ; Include DMPC chain topology
> #include "dmpc.itp"
> 
> ; Include water topology
> #include "gromos43a1_lipid.ff/spc.itp"
> 
> ; Include Position restraint file
> #ifdef POSRES_DRG
> #include "drg_posre.itp"
> #endif
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include topology for ions
> #include "gromos43a1_lipid.ff/ions.itp"
> 
> [ system ]
> ; Name
> drug in bilayer in water
> 
> 
> [ molecules ]
> ; Compound        #mols
> DRG         12
> DMPC        128
> SOL         1943
> CL          12
> 
> when:
> grompp -f NVT.mdp -c lip_12_ion_em.gro -p topol_drg.top -o nvt.tpr
> 
> Fatal error:
> [ file drg_posre.itp, line 28 ]:
> Atom index (24) in position_restraints out of bounds (1-23).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> 
> please guide me if its possile.

You have included the position restraints for the drug in two locations, one of 
which pertains to the water [moleculetype].  Please refer to the following for 
an example of exactly how to set up your topology:

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

Note that nearly all of the errors you might encounter will be explained on the 
same page.

-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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