Dear all; I am trying to constrain a double stranded DNA, I have made an index file and a posre.itp file, and then when I wanted to run grompp command I have encountered this: ........................................... Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1526
Fatal error: [ file posre_DNA.itp, line 318 ]: Atom index (314) in position_restraints out of bounds (1-313). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. ........................................................................... and the following lines are some parts of my .mdp file; ...................................................................................... title = DNA NVT equilibration define = -DPOSRES_DNA ; position restrain the DNA ; Run parameters integrator = md ; leap-frog integrator nsteps = 75000 ; 2 * 75000 = 150 ps ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = DNA Water_and_ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ......................................................................................... and my topl.top is the following lines; ; Include forcefield parameters #include "amber99.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_A.itp" #include "topol_DNA_chain_B.itp" #ifdef POSRES_DNA #include "posre_DNA.itp" #endif ; Include water topology #include "amber99.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber99.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols DNA_chain_A 1 DNA_chain_B 1 SOL 5580 NA 18 .............................................................................................. what do you suggest that I do to make it work? Thank you B.Mehrazma -- 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
