[gmx-users] genbox error

[Rini Gupta]

Dear gmx users,

I am using gromacs (version 4.0.7) 
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield.
I want to generate a box containing 20 BE and 480 water molecules using
genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. 

I used the following command:


genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7  -ci conf.gro -nmol 19 -maxsol 480 -o out.gro

Then  I got the mesaage:

Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration 
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 5699
Added 0 molecules (out of 19 requested) of G2
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 1992 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 8 x 8 x 8 cells
Succesfully made neighbourlist
nri = 10648, nrj = 270745
Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms.
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms.
Added 480 molecules
Generated solvent containing 1440 atoms in 480 residues
Writing generated configuration to out.gro


While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same.
I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20.

Can anyone please tell me what I am doing wrong here.

I using following topology file:

[ moleculetype ]
; Name   nrexcl
G269      3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OE    1    G2        OE     1   -0.345  15.9994
    2   CH2    1    G2        C      1    0.151  14.0270
    3   CH2    1    G2        C      1    0.194  14.0270      ;  0.000
    4   CH2    1    G2        C      2    0.231  14.0270
    5    OA    1    G2        O      2   -0.617  15.9994
    6     H    1    G2        H      2    0.386   1.0080      ;  0.000
    7   CH2    1    G2        C      3   -0.035  14.0270
    8   CH2    1    G2        C      3    0.143  14.0270
    9   CH3    1    G2        CA     3   -0.108  15.0350      ; -0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1430   8.1800e+06
    1    3    2   0.1430   8.1800e+06
    2    4    2   0.1520   5.4300e+06
    3    7    2   0.1520   5.4300e+06
    4    5    2   0.1430   8.1800e+06
    5    6    2   0.1000   2.3200e+07
    7    8    2   0.1530   7.1500e+06
    8    9    2   0.1530   7.1500e+06
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
    1    5    1
    1    8    1
    2    6    1
    2    7    1
    3    4    1
    3    9    1
[ angles ]
;  ai   aj   ak  funct   angle     fc
    2    1    3    2    109.50   380.00
    1    2    4    2    109.50   320.00
    1    3    7    2    109.50   320.00
    2    4    5    2    111.00   530.00
    4    5    6    2    108.53   443.00
    3    7    8    2    111.00   530.00
    7    8    9    2    111.00   530.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult
    3    1    2    4    1      0.00     1.26    3
    2    1    3    7    1      0.00     1.26    3
    1    2    4    5    1      0.00     2.53    3
    1    3    7    8    1      0.00     3.77    3
    2    4    5    6    1      0.00     1.26    3
    3    7    8    9    1      0.00     3.77    3
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions
                                     

Thanks and Regards,
Rini



----------------
Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver

 

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