[gmx-users] genbox error

[Mark Abraham]

On 12/02/2011 12:51 PM, Rini Gupta wrote:
>
> Hello Mark,
>
> Thanks for the reply.
>
> I tried to first make a box using editconf
> editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
>
> Box is successfully created and then I use
>
> genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro
>
> still, I am getting only one BE molecule instead of 19.

Hmm that's strange. What was the terminal output?

Mark

> What can I do now? Is there possibilty that my .gro file is not correct.
>
> Best Regards,
> Rini
>
> On Sat, 12 Feb 2011 06:58:49 +0530 wrote
> >
>
>
>
>
> On 12/02/2011 7:51 AM, 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
>
>
>
> 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.
>
>
>
>
> You're definitely trying to do too many things in one operation. I
> suggest
>
>
>
> 1. Use editconf to define a suitably big box around a single BE
> molecule.
>
>
>
> 2. Use genbox -ci -nmol 19
>
>
>
> 3. Use genbox -cs -cp
>
>
>
> Or use genconf -shuffle to replace 1 and 2 (but this is less random)
>
>
>
> Mark
>
>
>
>
>
>
> 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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>
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>
> -- 
>
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