Re: Re: [gmx-users] genbox error

Sat Feb 12 05:11:13 CET 2011

Hi,  

I am getting following output after using editconf to create  a box 
followed by
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 2 -o out.gro

This time i tried to insert just 2 molecules still the command is not 
working.

-------------------------------

Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/elements.dat
Entries in elements.dat: 218
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 19
Added 0 molecules (out of 2 requested) of G2
Writing generated configuration to out.gro

Back Off! I just backed up out.gro to ./#out.gro.1#
UNITED ATOM STRUCTURE FOR MOLECULE

Output configuration contains 9 atoms in 1 residues
Volume                 :      19.683 (nm^3)
Density                :     8.94928 (g/l)
Number of SOL molecules:      0   

Processing topology
--------------------------------------

Best Regards,
Rini

On Sat, 12 Feb 2011 08:07:27 +0530  wrote
>

    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

      -- 

      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

-- 

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/20110212/619a02ee/attachment.html>