[gmx-users] stopped simulation
Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. Kind regards, Ehsan -- 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] stopped simulation
Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Re: [gmx-users] stopped simulation
What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 11:22:09 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs
[gmx-users] .top file for a mixed solvent
Hi gmx users, I want to simulate ionomer is mixed solution of water and ethanol using gromos force field. I tired to follow the steps suggested on gromacs website, which are: 1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system. 2- Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro). 3- Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box. 4- Fill the remainder of the box with water (or whatever your other solvent is) using genbox. 5- Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system. Here are the commands that I used: pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top -i ionomer4.itp (ionomer-4.pdb is the pdb file for 4 ionomer molecule) pdb2gmx -f eth.pdb -o eth.gro -p eth.top -i eth.itp (eth.pdb is the pdb file for single ethanol molecule) editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -ci eth.gro -nmol 1000 -o phase1.gro genbox -cp phase1.gro -cs spc216.gro -o solvated.gro At the end, I have the solvated.gro file with 4 ionomer, 396 ethanol, and 423 water molecules. I don't know how to proceed step 5 and generated a combine .top file. What should I do with [ molecules ] directive? I appreciate any suggestions. Kind regards, Ehsan -- 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] problem vwith ethanol-water solution
Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? Kind regards, Ehsan -- 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] problem vwith ethanol-water solution
Thanks Justin, Here is the steps that I followed: pdb2gmx -f eth.pdb -o eth.gro -p eth.top pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro I got the box with ionomer in ethanol and water solution. However, I only have 400 of eth and 423 water molecule. The box wasn't large enough? What should I do with .top file? I have the .top file for ionomer and .top file for one eth molecule. Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 31, 2013 1:18:07 PM Subject: Re: [gmx-users] problem vwith ethanol-water solution On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added What did not work? In the absence of exact commands and description of the undesirable output, there's little to suggest from such statements. the nafion to the system, but these 3 molecules each sit a part from each other in the box in the pdb file. Any suggestion? http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] a new GROMACS simulation tool
Hi Kevin, It seems interesting. I would like to try it out. May I have an account? Best regards, Ehsan - Original Message - From: Kevin Chen fch6...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, October 22, 2013 7:34:10 AM Subject: [gmx-users] a new GROMACS simulation tool Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- 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 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] bonded interactions in Gromos96
Hi gromacs users, I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example: #define gb_10.1000 1.5700e+07 ; H - OA 750 The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750. The same story for the angle potential: #define ga_1 90.00 380.00 ; NR(heme) - FE - C 90 The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2 I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90. I appreciate if somebody could clarify this for me. Ehsan -- 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] double bond
Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms. I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? Regards, Ehsan -- 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] double bond
Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software? Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 3, 2013 1:09:05 PM Subject: Re: [gmx-users] double bond On 10/3/13 3:08 PM, Ehsan Sadeghi wrote: Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms. I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? There is no distinction between a single, double, or triple bond in an MM force field, and Gromacs certainly doesn't change anything about the bonds. If your desired geometry isn't being preserved, choose or derive better bonded parameters. Also note that bonds will not break; visualization software often guesses bonds incorrectly. What you see is not definitive. What is written in the topology is. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] ionomer topolgy
Thanks Justin, I modified the pdb file, but it cannot recognize my residue LIG. Here is the error: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion5.pdb... Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 2 residues with 46 atoms chain #res #atoms 1 ' ' 2 46 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.41# Processing chain 1 (46 atoms, 2 residues) Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LIG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 5:50:00 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 8:43 PM, Ehsan Sadeghi wrote: Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff. I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right? Yes you did; you modified the Gromos96 53A6 force field. There's nothing wrong with that; it's precisely what you wanted to do. Also note that there is no such thing as a default force field. Here is the output from pdb2gmx. Thank you for your consideration. --- Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion3.pdb... WARNING: all CONECT records are ignored Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 0 residues with 46 atoms chain #res #atoms 1 'G' 1 24 2 'H' 1 22 WARNING: there were 1 atoms with zero occupancy and 45 atoms with occupancy unequal to one (out of 46 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.36# Processing chain 1 'G' (24 atoms, 1 residues) Warning: Starting residue LI0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642
Re: [gmx-users] ionomer topolgy
Yes, I have introduced the new .rtp entry in /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. What could be wrong? - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 30, 2013 11:16:57 AM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 12:50 PM, Ehsan Sadeghi wrote: Thanks Justin, I modified the pdb file, but it cannot recognize my residue LIG. Here is the error: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion5.pdb... Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 2 residues with 46 atoms chain #res #atoms 1 ' ' 2 46 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.41# Processing chain 1 (46 atoms, 2 residues) Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LIG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You have introduced the new .rtp entry in the correct file, right? That is, you have modified /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] ionomer topolgy
I was pretty confident that I am modifying the right file. apparently I did not access to the main file; so I asked my supervisor and he provided me with a proper access to the files. Thanks again Justin. - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 30, 2013 1:45:41 PM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 4:40 PM, Ehsan Sadeghi wrote: Many thanks Justin. Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling. In the future, make sure you're providing accurate answers to the questions being asked. I asked about this at least two or three times and was always assured that the modifications were being done properly. If you want free help, you have to make it easy! I also have some concern about my pdb file. i generated from my drawing in Avogadro, with some arbitrary bond length and angle. I hope that I can find the correct bond length and angle with energy minimization; am, I right? If done in vacuo, probably. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] ionomer topolgy
Many thanks Justin. Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling. I also have some concern about my pdb file. i generated from my drawing in Avogadro, with some arbitrary bond length and angle. I hope that I can find the correct bond length and angle with energy minimization; am, I right? Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 30, 2013 11:27:25 AM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 2:23 PM, Ehsan Sadeghi wrote: Yes, I have introduced the new .rtp entry in /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. What could be wrong? The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would not throw that error. Can you provide the output of: grep LIG /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -Justin - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 30, 2013 11:16:57 AM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 12:50 PM, Ehsan Sadeghi wrote: Thanks Justin, I modified the pdb file, but it cannot recognize my residue LIG. Here is the error: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion5.pdb... Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 2 residues with 46 atoms chain #res #atoms 1 ' ' 2 46 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.41# Processing chain 1 (46 atoms, 2 residues) Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LIG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You have introduced the new .rtp entry in the correct file, right? That is, you have modified /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] ionomer topolgy
Hello Gromacs users, I am the beginner in Gromacs. I want to simulate ionomer in water. I could not find a pdb file for my case, and I tried to draw the ionomer in Avogadro software and generated the pdb file. However, gmx cannot find my residue names. I added my residue name to residuetypes.dat and added the residue in aminoacids.rtp in gromos. I does not work and it cannot find my new residue. What should I do? I also have some question regarding the .rtp file. Do you I need to include [ bonds] , [angles], [dihedrals] as well? How can I find charge and charge groups in the [ atoms] section. Thanks 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] ionomer topolgy
CONECT 149 CONECT 15 12 18 19 20 CONECT 15 CONECT 16 12 CONECT 17 12 CONECT 18 15 23 24 25 CONECT 18 CONECT 19 15 CONECT 20 15 CONECT 211 CONECT 221 CONECT 23 18 CONECT 24 18 CONECT 25 18 26 CONECT 26 25 27 28 29 CONECT 26 CONECT 27 26 30 31 32 CONECT 27 CONECT 28 26 CONECT 29 26 CONECT 30 27 33 34 35 CONECT 30 CONECT 31 27 36 CONECT 32 27 CONECT 33 30 CONECT 34 30 CONECT 35 30 CONECT 36 31 37 38 39 CONECT 36 CONECT 37 36 40 41 42 CONECT 37 CONECT 38 36 CONECT 39 36 CONECT 40 37 43 45 46 CONECT 40 CONECT 41 37 CONECT 42 37 CONECT 43 40 44 CONECT 44 43 CONECT 45 40 CONECT 46 40 MASTER00000000 460 460 END - I already added LIG and SCH in residuetypes.dat and defined the atoms for each residue in aminoacids.rtp in gromos. When I run pdb2gmx -f nafion.pdb I receive this error: Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LIG' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS Thank you, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 11:50:13 AM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 2:34 PM, Ehsan Sadeghi wrote: Hello Gromacs users, I am the beginner in Gromacs. I want to simulate ionomer in water. I could not find a pdb file for my case, and I tried to draw the ionomer in Avogadro software and generated the pdb file. However, gmx cannot find my residue names. I added my residue name to residuetypes.dat and added the residue in aminoacids.rtp in gromos. I does not work and it cannot find my new residue. What should I do? Well, there are several Gromos parameter sets; have you modified and then chosen the correct one? In the absence of more detail, it's hard to figure out what's gone wrong. I also have some question regarding the .rtp file. Do you I need to include [ bonds] , [angles], [dihedrals] as well
Re: [gmx-users] ionomer topolgy
Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O CONECT12 21 22 CONECT21345 CONECT2 CONECT32678 CONECT3 CONECT42 CONECT52 CONECT639 10 11 CONECT6 CONECT73 CONECT83 CONECT96 12 13 14 CONECT9 CONECT 106 CONECT 116 CONECT 129 15 16 17 CONECT 12 CONECT 139 CONECT 149 CONECT 15 12 18 19 20 CONECT 15 CONECT 16 12 CONECT 17 12 CONECT 18 15 23 24 25 CONECT 18 CONECT 19 15 CONECT 20 15 CONECT 211 CONECT 221 CONECT 23 18 CONECT
Re: [gmx-users] ionomer topolgy
Thanks Justin. I try to modify my file based on your comments. - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 1:24:44 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 4:18 PM, Ehsan Sadeghi wrote: Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Your definition of LIG in the .rtp entry does not come anywhere close to matching what is in the .pdb file. If, in fact, each residue only has two atoms (I don't see how that's chemically possible), then your residue numbers have to follow suit. As it stands now, pdb2gmx is trying to find a 24-atom LIG residue and a 22-atom SCH. Neither of these is true, per the .rtp. -Justin Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772
Re: [gmx-users] ionomer topolgy
0.000 0 F6 F 0.000 0 C4 C 0.000 0 C5 C 0.000 0 F7 F 0.000 0 F8 F 0.000 0 S S 0.000 0 F9 F 0.000 0 F10F 0.000 0 O3 O 0.000 0 H H 0.000 0 O4 O 0.000 0 O5 O 0.000 0 Thanks, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 1:24:44 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 4:18 PM, Ehsan Sadeghi wrote: Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Your definition of LIG in the .rtp entry does not come anywhere close to matching what is in the .pdb file. If, in fact, each residue only has two atoms (I don't see how that's chemically possible), then your residue numbers have to follow suit. As it stands now, pdb2gmx is trying to find a 24-atom LIG residue and a 22-atom SCH. Neither of these is true, per the .rtp. -Justin Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00
Re: [gmx-users] ionomer topolgy
Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff. I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right? Here is the output from pdb2gmx. Thank you for your consideration. --- Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion3.pdb... WARNING: all CONECT records are ignored Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 0 residues with 46 atoms chain #res #atoms 1 'G' 1 24 2 'H' 1 22 WARNING: there were 1 atoms with zero occupancy and 45 atoms with occupancy unequal to one (out of 46 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.36# Processing chain 1 'G' (24 atoms, 1 residues) Warning: Starting residue LI0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LI' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 3:06:05 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 5:53 PM, Ehsan Sadeghi wrote: Hello, I revised my pdb and rtp files. I still receive similar error message. Whatever modifications you're making probably aren't being done in the right files. You haven't yet responded to my question about which force field you're using and whether you're making modifications in the working directory or in $GMXLIB. Exact screen output from pdb2gmx would be very useful here. Please post the exact command and all screen output, including your selections and the error message. -Justin Here are the new files: .pdb: ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C3LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F1LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F2LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C4LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F3LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F4LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C5LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F5LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F6LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C6LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F7LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F8LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C7LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F9LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F10 LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C8LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F11 LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F12 LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21
