[gmx-users] Coulomb Energy
Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-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
[gmx-users] Information about boxX,boxY e boxZ
Dear All I run a 1ns MD on a membrane protein and I get these values for box coordinate's Energy Average Err.Est. RMSD Tot-Drift --- Box-X 13.867 0.071 0.167634 0.48292 (nm) Box-Y 13.867 0.071 0.167634 0.48292 (nm) Box-Z 9.15929 0.095 0.222463 -0.642479 (nm) BoxX and BoxY fluctuate between 13,5 and 14,2 nm , BoxZ fluctuate between 8,6 e 9,6 nm. These values seem not to reach a convergence. Which could be the cause? How can I fix it? Thanks-- gmx-users mailing listgmx-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
Re: [gmx-users] Coulomb Energy
On 18/12/2011 7:41 PM, Saba Ferdous wrote: Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Nothing. The fact that it is convenient to compute and report those terms separately doesn't mean there's any connection with a useful observable. Force fields are parametrized to reproduce some experimental and/or computational data. There's no a priori reason to suppose that bits and pieces of the force field in isolation have any particular connection to any such observable. Mark Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-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
Re: [gmx-users] Information about boxX,boxY e boxZ
On 18/12/2011 8:00 PM, Alex Jemulin wrote: Dear All I run a 1ns MD on a membrane protein and I get these values for box coordinate's EnergyAverageErr.Est.RMSDTot-Drift --- Box-X13.8670.0710.1676340.48292(nm) Box-Y13.8670.0710.1676340.48292(nm) Box-Z9.159290.0950.222463-0.642479(nm) BoxX and BoxY fluctuate between 13,5 and 14,2 nm , BoxZ fluctuate between 8,6 e 9,6 nm. These values seem not to reach a convergence. Which could be the cause? How can I fix it? Does your experience of the membrane simulation literature suggest that equilibration normally occurs over 1ns? In the absence of any description of the starting point or procedure you used, nobody will be able to say anything. Mark -- gmx-users mailing listgmx-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
[gmx-users] LINCS error
Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces 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 = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- gmx-users mailing listgmx-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
Re: [gmx-users] LINCS error
On 19/12/2011 1:05 AM, aiswarya pawar wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation for general advice. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5000; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces 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= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc = xyz; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 You are asking for trouble by generating velocities and doing position restraints with P-R pressure coupling in one step. It might work, but the workflow in the above link is safer. and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 Why are you re-generating non-equilibrium velocities after equilibrating them? Mark The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- gmx-users mailing listgmx-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
[gmx-users] Invitation to connect on LinkedIn
LinkedIn ram prasad requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - ram Accept invitation from ram prasad http://www.linkedin.com/e/-85v1n9-gwcabl25-x/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I62326946_16/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dz5vdzgVdz8Pczp9bORRhDFhcjhJbPgOdz8PdzcUdj8LrCBxbOYWrSlI/EML_comm_afe/?hs=falsetok=0dNijIAs-HN501 View invitation from ram prasad http://www.linkedin.com/e/-85v1n9-gwcabl25-x/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I62326946_16/0SclYSd3ASczcOdAALqnpPbOYWrSlI/svi/?hs=falsetok=2ciLjt_iSHN501 -- Why might connecting with ram prasad be a good idea? ram prasad's connections could be useful to you: After accepting ram prasad's invitation, check ram prasad's connections to see who else you may know and who you might want an introduction to. Building these connections can create opportunities in the future. -- (c) 2011, LinkedIn Corporation-- gmx-users mailing listgmx-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
[gmx-users] maxh not causing termination
I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Cheers, Ben -- gmx-users mailing listgmx-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
[gmx-users] regarding x2top error
hello sir, i tried to produce rtp file using x2top command for my file HETATM 123 C BFC A 1 0.446 -0.085 2.419 1.00 0.00 C HETATM 124 O BFC A 1 0.234 -0.665 3.482 1.00 0.00 O HETATM 125 CA BFC A 1 1.485 -0.637 1.467 1.00 0.00 C HETATM 126 CB BFC A 1 1.895 0.310 0.300 1.00 0.00 C HETATM 127 OB BFC A 1 0.871 0.428 -0.648 1.00 0.00 O HETATM 128 CC BFC A 1 3.158 -0.281 -0.373 1.00 0.00 C HETATM 129 CD BFC A 1 3.913 0.725 -1.260 1.00 0.00 C HETATM 130 CE BFC A 1 4.740 1.741 -0.452 1.00 0.00 C HETATM 131 CF BFC A 1 5.487 2.778 -1.309 1.00 0.00 C HETATM 132 CG BFC A 1 4.591 3.814 -2.015 1.00 0.00 C HETATM 133 CH BFC A 1 3.801 4.715 -1.053 1.00 0.00 C HETATM 134 CI BFC A 1 2.988 5.801 -1.771 1.00 0.00 C HETATM 135 CJ BFC A 1 2.160 6.653 -0.799 1.00 0.00 C HETATM 136 CK BFC A 1 1.328 7.736 -1.500 1.00 0.00 C HETATM 137 CL BFC A 1 0.560 8.633 -0.516 1.00 0.00 C HETATM 138 CM BFC A 1 -0.302 9.699 -1.195 1.00 0.00 C HETATM 139 HA1 BFC A 1 1.124 -1.605 1.056 1.00 0.00 H HETATM 140 HA2 BFC A 1 2.392 -0.853 2.076 1.00 0.00 H HETATM 141 HB BFC A 1 2.141 1.308 0.723 1.00 0.00 H HETATM 142 HC1 BFC A 1 2.862 -1.163 -0.985 1.00 0.00 H HETATM 143 HC2 BFC A 1 3.865 -0.642 0.407 1.00 0.00 H HETATM 144 HD1 BFC A 1 3.187 1.254 -1.912 1.00 0.00 H HETATM 145 HD2 BFC A 1 4.611 0.159 -1.917 1.00 0.00 H HETATM 146 HE1 BFC A 1 5.500 1.172 0.131 1.00 0.00 H HETATM 147 HE2 BFC A 1 4.095 2.266 0.282 1.00 0.00 H HETATM 148 HF1 BFC A 1 6.091 2.242 -2.076 1.00 0.00 H HETATM 149 HF2 BFC A 1 6.198 3.330 -0.654 1.00 0.00 H HETATM 150 HG1 BFC A 1 3.885 3.296 -2.697 1.00 0.00 H HETATM 151 HG2 BFC A 1 5.246 4.463 -2.639 1.00 0.00 H HETATM 152 HH1 BFC A 1 4.510 5.203 -0.347 1.00 0.00 H HETATM 153 HH2 BFC A 1 3.098 4.091 -0.457 1.00 0.00 H HETATM 154 HI1 BFC A 1 2.301 5.317 -2.498 1.00 0.00 H HETATM 155 HI2 BFC A 1 3.682 6.462 -2.337 1.00 0.00 H HETATM 156 HJ1 BFC A 1 2.846 7.138 -0.069 1.00 0.00 H HETATM 157 HJ2 BFC A 1 1.471 5.988 -0.230 1.00 0.00 H HETATM 158 HK1 BFC A 1 0.600 7.244 -2.181 1.00 0.00 H HETATM 159 HK2 BFC A 1 2.004 8.371 -2.115 1.00 0.00 H HETATM 160 HL1 BFC A 1 1.291 9.135 0.158 1.00 0.00 H HETATM 161 HL2 BFC A 1 -0.094 7.990 0.114 1.00 0.00 H HETATM 162 HM1 BFC A 1 0.328 10.382 -1.806 1.00 0.00 H HETATM 163 HM2 BFC A 1 -0.840 10.303 -0.434 1.00 0.00 H HETATM 164 HM3 BFC A 1 -1.054 9.220 -1.859 1.00 0.00 H i used g_x2top -f fattyacid.pdb -o out.top -r out.rtp -nopbc command. but i got error as * There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 42 Can not find forcefield for atom C-1 with 2 bonds --- Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 41 out of 42 atoms.* i dono how to resolve this . can anyone pls tell me how to solve tis. i checked my .n2t file also. but i couldnt get the error. help me with your answer ... thanking you, -- gmx-users mailing listgmx-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
Re: [gmx-users] regarding x2top error
On 2011-12-19 07:15, priya thiyagarajan wrote: hello sir, i tried to produce rtp file using x2top command for my file HETATM 123 C BFC A 1 0.446 -0.085 2.419 1.00 0.00 C HETATM 124 O BFC A 1 0.234 -0.665 3.482 1.00 0.00 O HETATM 125 CA BFC A 1 1.485 -0.637 1.467 1.00 0.00 C HETATM 126 CB BFC A 1 1.895 0.310 0.300 1.00 0.00 C HETATM 127 OB BFC A 1 0.871 0.428 -0.648 1.00 0.00 O HETATM 128 CC BFC A 1 3.158 -0.281 -0.373 1.00 0.00 C HETATM 129 CD BFC A 1 3.913 0.725 -1.260 1.00 0.00 C HETATM 130 CE BFC A 1 4.740 1.741 -0.452 1.00 0.00 C HETATM 131 CF BFC A 1 5.487 2.778 -1.309 1.00 0.00 C HETATM 132 CG BFC A 1 4.591 3.814 -2.015 1.00 0.00 C HETATM 133 CH BFC A 1 3.801 4.715 -1.053 1.00 0.00 C HETATM 134 CI BFC A 1 2.988 5.801 -1.771 1.00 0.00 C HETATM 135 CJ BFC A 1 2.160 6.653 -0.799 1.00 0.00 C HETATM 136 CK BFC A 1 1.328 7.736 -1.500 1.00 0.00 C HETATM 137 CL BFC A 1 0.560 8.633 -0.516 1.00 0.00 C HETATM 138 CM BFC A 1 -0.302 9.699 -1.195 1.00 0.00 C HETATM 139 HA1 BFC A 1 1.124 -1.605 1.056 1.00 0.00 H HETATM 140 HA2 BFC A 1 2.392 -0.853 2.076 1.00 0.00 H HETATM 141 HB BFC A 1 2.141 1.308 0.723 1.00 0.00 H HETATM 142 HC1 BFC A 1 2.862 -1.163 -0.985 1.00 0.00 H HETATM 143 HC2 BFC A 1 3.865 -0.642 0.407 1.00 0.00 H HETATM 144 HD1 BFC A 1 3.187 1.254 -1.912 1.00 0.00 H HETATM 145 HD2 BFC A 1 4.611 0.159 -1.917 1.00 0.00 H HETATM 146 HE1 BFC A 1 5.500 1.172 0.131 1.00 0.00 H HETATM 147 HE2 BFC A 1 4.095 2.266 0.282 1.00 0.00 H HETATM 148 HF1 BFC A 1 6.091 2.242 -2.076 1.00 0.00 H HETATM 149 HF2 BFC A 1 6.198 3.330 -0.654 1.00 0.00 H HETATM 150 HG1 BFC A 1 3.885 3.296 -2.697 1.00 0.00 H HETATM 151 HG2 BFC A 1 5.246 4.463 -2.639 1.00 0.00 H HETATM 152 HH1 BFC A 1 4.510 5.203 -0.347 1.00 0.00 H HETATM 153 HH2 BFC A 1 3.098 4.091 -0.457 1.00 0.00 H HETATM 154 HI1 BFC A 1 2.301 5.317 -2.498 1.00 0.00 H HETATM 155 HI2 BFC A 1 3.682 6.462 -2.337 1.00 0.00 H HETATM 156 HJ1 BFC A 1 2.846 7.138 -0.069 1.00 0.00 H HETATM 157 HJ2 BFC A 1 1.471 5.988 -0.230 1.00 0.00 H HETATM 158 HK1 BFC A 1 0.600 7.244 -2.181 1.00 0.00 H HETATM 159 HK2 BFC A 1 2.004 8.371 -2.115 1.00 0.00 H HETATM 160 HL1 BFC A 1 1.291 9.135 0.158 1.00 0.00 H HETATM 161 HL2 BFC A 1 -0.094 7.990 0.114 1.00 0.00 H HETATM 162 HM1 BFC A 1 0.328 10.382 -1.806 1.00 0.00 H HETATM 163 HM2 BFC A 1 -0.840 10.303 -0.434 1.00 0.00 H HETATM 164 HM3 BFC A 1 -1.054 9.220 -1.859 1.00 0.00 H i used g_x2top -f fattyacid.pdb -o out.top -r out.rtp -nopbc command. but i got error as Your model is incomplete. The first carbon has only two bonds, to O and C. * There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 42 Can not find forcefield for atom C-1 with 2 bonds --- Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 41 out of 42 atoms.* i dono how to resolve this . can anyone pls tell me how to solve tis. i checked my .n2t file also. but i couldnt get the error. help me with your answer ... thanking you, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
