Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is
#include "amber99sb.ff/forcefield.itp" #include "my_ligand_atomtypes.itp" ; Include chain topologies #include "A.itp" #ifdef POSRES #include "posre_A.itp" #endif #include "B.itp" #ifdef POSRES #include "posre_B.itp" #endif ; Include custom ligand topologies #include "npd.itp" #ifdef POSRES_LIG #include "posre_npd.itp" #endif ; Include custom ligand topologies #include "ir3_em.itp" ; Include water topology #include "amber99sb.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 generic ion topology #include "amber99sb.ff/ions.itp" [ system ] ; Name BcSIRED in water [ molecules ] ; Compound #mols A 1 B 1 NPD 1 IR3 9 SOL 123406 NA 24 then I have my_ligand_atomtypes.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700 P P 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; IR3_GMX.top created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015 ; Include forcefield parameters [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 My first ligand gro file GRoups of Organic Molecules in ACtion for Science 73 1NPD OA22 1 -0.282 0.251 -5.719 1NPD OA23 2 -0.142 0.366 -5.542 1NPD OA24 3 -0.039 0.314 -5.771 1NPD P'A2 4 -0.145 0.285 -5.669 1NPD PA 5 -0.033 -0.056 -5.010 1NPD PN 6 -0.130 -0.245 -4.804 1NPD O3P 7 -0.126 -0.116 -4.893 1NPD N1A 8 -0.692 0.110 -5.840 1NPD N1N 9 -0.539 -0.355 -4.443 1NPD C2A 10 -0.613 0.000 -5.836 ... 1NPD H8A 73 -0.376 0.292 -5.440 1.94588 0.88647 1.08377 My second ligand gro file IR3_GMX.gro created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015 22 1IR3 CAA 1 10.182 10.576 10.387 1IR3 HAB 2 10.211 10.640 10.305 1IR3 HAA 3 10.075 10.577 10.396 .... 1IR3 HAF 22 10.581 10.138 10.385 20.72517 20.72517 20.72517 but the system can`t go under energy minimization. This is my em.mdp title = Minimization ; Title of run integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 500000 ; Maximum number of (minimization) steps to perform energygrps = Protein NPD IR3 ; Which energy group(s) to write to disk nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions I change emtol from 1000, then 500, then 100. No error generated but the pdb output file goes wrong with the ligands. If I do the same procedure with seperated ligand (only one [ atomtypes] in my_ligand_atomtypes.itp), things goes well . Could you please help me where is the problem? Many thanks in advance. Jennifer -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.