[gmx-users] genbox error

[Justin A. Lemkul]

Rini Gupta wrote:
> 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
> 

Do the -ci and -cs steps separately and see if that gives you the proper output. 
  I have found that the two are incompatible, but in theory, I don't know why 
one couldn't do everything in one step.

-Justin

> 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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> 

-- 
========================================

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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