[gmx-users] solvent group size (12548) is not a multiple of 3

[Terry]

On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap <sangita at imtech.res.in>wrote:

>
> Hello all
> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
> I am geeting error during addiotion of ions
> Fatal error:
> Your solvent group size (12548) is not a multiple of 3
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I have done following:
>
> GROMACS COMMAND
>
> 1) Generate topol.top using GROMOS96 53A6 parameter set
> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
>
> ay prompt select 13, 2, 2
>
> 2) Download:
>    * dppc128.pdb - the structure of a 128-lipid DPPC bilayer
>    * dppc.itp - the moleculetype definition for DPPC
>    * lipid.itp - Berger lipid parameters
>
> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> 3) Modify topol.top with:
> #include "gromos53a6.ff/forcefield.itp"
>
> to:
>
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
>
>                &
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
>
>
> 4) cp files
> aminoacids.rtp
> aminoacids.hdb
> aminoacids.c.tdb
> aminoacids.n.tdb
> aminoacids.r2b
> aminoacids.vsd
> ff_dum.itp
> ffnonbonded.itp
> ffbonded.itp
> forcefield.itp
> ions.itp
> spc.itp
> watermodels.dat
>
> from gromacs top to directory named gromos53a6_lipid.ff in working
> directory.
> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
> lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc
> file
> that contains a description of the force field parameters contain
> "GROMOS96 53A6
> force field, extended to include Berger lipid parameters".
> Delete line ";; parameters for lipid-GROMOS interactions." and its
> subsequent
> line, change HW as H of [ nonbond_params ]
>
>
> 5) Generate .tpr for POPC
> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
>
>
> 6) Remove periodicity
> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur
> compact
> (at command prompt select 0)
>
>
> 7) Oriant the KALP peptide within the same coordinate as written in end of
> popc128a_whole.gro
> editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910
> 6.17970
> 6.91950
>
>
> 8) Pack lipid around protein
> cat KALP_newbox.gro popc128a_whole.gro > system.gro
> Remove unnecessary lines (the box vectors from the KALP structure, the
> header
> information from the DPPC structure) and update the second line of the
> coordinate file (total number of atoms) accordingly.
>
>
> 9) Modify topol.top to add positional restrain on protein
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
>             &
>
> Genrate new positional restraint
> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> (at prompt select 2)
>
> Add a line "define = -DSTRONG_POSRES" to .mdp file
>
>
>
>
> 10) Scale down lipid
> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5
> area_shrink1.dat
> system_shrink1.gro
>
>
> 11) addion POPC 128 to topol.top
>
>
> 12) Solvate with water
> Copy vdwradii.dat from Gromacs top to working directory and change the
> value of
> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>
> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
> topol.top
>
>
> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr
>
> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
> CL -nn 4
> (at command prompt select 0)
>

Is group 0 your solvent? You should chose a group corresponding to the
solvent of your system.



>
>
>
> So can anyone please help me correct this error.
>
>
>
> With regards
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
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