Re:[gmx-users] genbox error

Sat Feb 12 02:51:54 CET 2011

 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.

 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

-- 

gmx-users mailing list  gmx-users at gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users

Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

Please don't post (un)subscribe requests to the list. Use the 

www interface or send it to gmx-users-request at gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110212/d68e6f55/attachment.html>