On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap <sang...@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 > > ______________________________________________________________________ > 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 >
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