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 ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists