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

[Sangita Kachhap]

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)



So can anyone please help me correct this error.



With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH

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