Re: [gmx-users] LIGAND TOPOLOGY
On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote: Dear users, I have been trying to build la ligand topology of my ligand through the PRODRG web server. I have the following queries; According to Justin's important tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html i am lost on how to allocate equivalent charges to equivalent groups. I have read the recommended paper but seems still i have issues in allocating the correct charges to my groups. You'll have to be a lot more specific with what you're dealing with and what you're doing if you want to get any useful help. Secondly, its about how to determine which groups are encompassed by a charge group Attached find in my PRODRG input file. Attachments are not allowed on the mailing list. Someone out there help me in understanding this. Charge groups are used in the Gromos96 force fields and typically contain 2-4 atoms such that the group has an integral charge (generally -1, 0, or 1). Figures 1, 3, 4, and 5 of our paper (dx.doi.org/10.1021/ci100335w) show how to properly assign charge groups in molecules of increasing complexity. Our work should have encompassed almost all of the most commonly encountered functional groups. Other examples for well-known molecules can be found in the .rtp file for the force field. -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] Re: topology and coordinate file not matching after grompp
Hi Justin, The simulation is running fine for this task. There's something additional I want to do and I'd like to know how you'd approach it. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective charge cloud. The proteins im using are 2CDS.pdb and 1AKI.pdb from the RCSB bank. From what I figured, I tried using genion under the impression that I could replace the solvent molecules with CL ions but I don't think this worked. I'd really appreciate it if you could share your thoughts on this Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010334.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
Hi Justin, The simulation is running fine for this task. Thank you for helping me There's something additional I want to do and I'd like to know how you'd approach it. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective charge cloud. The proteins im using are 2CDS.pdb and 1AKI.pdb from the RCSB bank. From what I figured, I tried using genion under the impression that I could replace the solvent molecules with CL ions but I don't think this worked. I'd really appreciate it if you could share your thoughts on this Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 8/5/13 5:39 AM, chinnu657 wrote: Hi Justin, The simulation is running fine for this task. Thank you for helping me There's something additional I want to do and I'd like to know how you'd approach it. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective charge cloud. The proteins im using are 2CDS.pdb and 1AKI.pdb from the RCSB bank. From what I figured, I tried using genion under the impression that I could replace the solvent molecules with CL ions but I don't think this worked. I'd really appreciate it if you could share your thoughts on this I don't see how adding ions into the solvent would help you understand anything about changing charges on the protein. Please start a new thread if you're introducing a new topic for discussion. -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] Re: topology and coordinate file not matching after grompp
oh, sorry. So the error is: Fatal error: Topology include file posre.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr My topol.top: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #ifdef POSRES #include posre_1AKI.itp #endif #include topol_2CDS.itp #ifdef POSRES #include posre_2CDS.itp #endif ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] #mols Protein_1AKI1 Protein_2CDS1 SOL 27020 CL- 16 -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010309.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 8/2/13 5:57 AM, chinnu657 wrote: oh, sorry. So the error is: Fatal error: Topology include file posre.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors There are probably #include statements in the .itp files for the proteins, since they were originally .top files written by pdb2gmx. You'll need to get rid of those or otherwise suitably rename them (and then delete the redundant #include statements in the .top). -Justin The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr My topol.top: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #ifdef POSRES #include posre_1AKI.itp #endif #include topol_2CDS.itp #ifdef POSRES #include posre_2CDS.itp #endif ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] #mols Protein_1AKI1 Protein_2CDS1 SOL 27020 CL- 16 -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010309.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] Re: topology and coordinate file not matching after grompp
Hi Justin, Yes that was a problem. So after modifying my #include statement in the itp file (initially top. file), it became: ; Include Position restraint file #ifdef POSRES #include posre_2CDS.itp #endif thank you Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010312.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a new top file was made in which the itp files were included. I pasted the contents earlier. After this, performed editconf separately on each .gro file and combined them together. then I solvated them. Right before neutralising using genion, while using grompp to get the tpr file is where the error about the mismatch happens. How can I solve this? I've tried making sure my topology file is updated at every stage. Kind Regards, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010236.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 10:07 AM, chinnu657 wrote: Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a new top file was made in which the itp files were included. I pasted the contents earlier. After this, performed editconf separately on each .gro file and combined them together. then I solvated them. Right before neutralising using genion, while using grompp to get the tpr file is where the error about the mismatch happens. How can I solve this? I've tried making sure my topology file is updated at every stage. The most common source of problem is water molecules not being accurately accounted for, but the difference cited in the error message is 20, so it's probably not the waters. I can't tell based on the description exactly what you did. As I said before, an exact sequence of commands (copied and pasted from the terminal) is helpful. Concatenating coordinate files is precarious, as you have to conduct manual deletions of lines to fix them after combining them. -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] Re: topology and coordinate file not matching after grompp
Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro system.gro genconf -f system.gro -o renumber.gro -renumber editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr It is after this that I get the error Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010244.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 11:29 AM, chinnu657 wrote: Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro system.gro genconf -f system.gro -o renumber.gro -renumber editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr It is after this that I get the error If you send me renumber.gro and both protein .itp files (off-list), I will have a look and try to figure out where the problem lies. In theory, the above commands should work, provided that the modifications following concatenation were correct, though if genconf didn't complain, whatever you did is probably fine, at least from a syntactical standpoint if not a topological one. -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] Re: topology and coordinate file not matching after grompp
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro topol_1AKI.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp topol_2CDS.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp I get the feeling you're not going to be able to see the files that I have uploaded here. If you prefer, I can send it to your personal email :) Thank you for your help and the time your putting.. I have attached allt eh files you asked for. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010247.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 11:59 AM, chinnu657 wrote: renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro topol_1AKI.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp topol_2CDS.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp I get the feeling you're not going to be able to see the files that I have uploaded here. If you prefer, I can send it to your personal email :) Thank you for your help and the time your putting.. I have attached allt eh files you asked for. You've chopped off part of your protein: 257ARGNH2 3896 8.875 0.492 -2.033 0. 0. 0. 257ARG HH21 3897 8.820 0.535 -1.961 0. 0. 0. 257ARG HH22 3898 8.854 0.511 -2.129 0. 0. 0. 257ARG C 3899 8.936 0.127 -1.437 0. 0. 0. 257ARG O 3900 8.881 0.230 -1.398 0. 0. 0. 8.63000 4.23400 4.31000 There are 129 residues and 1960 atoms in both proteins, thus you should have 3920 atoms total. You have lost the last Leu residue from the second protein, which accounts for your missing atoms. -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] Re: topology and coordinate file not matching after grompp
Thank you very much Justin. It's working fine now :) Really appreciate it. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010255.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file posre.itp not found. In my topology file I wrote this: ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ; Include Position restraint file #ifdef POSRES #include 1AKI_posre.itp #include 2CDS_posre.itp #endif If the problem is that I need to strictly make it #include posre.itp, then how do I combine the two posre.itp files together? chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010256.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 2:48 PM, chinnu657 wrote: I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file posre.itp not found. In my topology file I wrote this: ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ; Include Position restraint file #ifdef POSRES #include 1AKI_posre.itp #include 2CDS_posre.itp #endif If the problem is that I need to strictly make it #include posre.itp, then how do I combine the two posre.itp files together? You don't. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -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] Re: topology and coordinate file not matching after grompp
Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010259.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 3:10 PM, chinnu657 wrote: Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. Without the command issued, exact error message (copied and pasted from the terminal), and relevant topology snippet, there's nothing anyone can do to help aside from telling you whatever you did is still wrong. Please be as explicit as possible to arrive at a conclusion. -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] Generate topology
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Thanks in advance, Afsaneh -- 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] Generate topology
On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory. -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] Generate topology
Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. thanks in advance, Afsaneh -- 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] Generate topology
On 7/19/13 9:10 AM, afsaneh maleki wrote: Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. What error? -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] Generate topology -2
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I edited atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms for more information and tips for troubleshooting, ……….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? Thanks in advance, Afsaneh -- 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] Generate topology -2
On 7/19/13 9:32 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I edited atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms for more information and tips for troubleshooting, ……….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? Let's not go backwards. I responded to this post already and you gave a cryptic reply about some new error. Please respond to the other post. -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
Re: [gmx-users] Generate topology
Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory. I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……….. I seem can't read atomname2type.n2t file from my working directory. Thanks very much. Afsaneh On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Generate topology
On 7/19/13 10:06 AM, afsaneh maleki wrote: Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory. I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……….. I seem can't read atomname2type.n2t file from my working directory. Use -ff select to choose the force field that resides in the working directory. Specifying -ff oplsaa tells g_x2top to use the oplsaa.ff directory in $GMXLIB. -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] namd2gmx topology conversion tool
Dear Gromacs users! I have some topologies made for NAMD (param files) which I'd like convert to the Gromacs itp formats. Could someone provide me with some tools for such conversion? Thanks for help, James -- 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] About Topology construction for CNT wrapped by Cyclic peptide
Dear Justin , Thank you for your reply, I need to construct Topology For Carbon Nano tubes (CNT) in gromoff53a5.ff . For that When i run the Following Command ./g_x2top_d -f CNT.gro -o CNT.top -r CNT.rtp I have got Error as follows Can not find forcefield for atom N-325 with 0 bonds Can not find forcefield for atom CA-326 with 2 bonds Can not find forcefield for atom CB-327 with 2 bonds Can not find forcefield for atom CG-328 with 2 bonds Can not find forcefield for atom C-330 with 2 bonds Can not find forcefield for atom O-331 with 1 bonds Can not find forcefield for atom N-332 with 0 bonds Can not find forcefield for atom C-836 with 3 bonds Can not find forcefield for atom C-837 with 3 bonds Can not find forcefield for atom C-838 with 2 bonds Can not find forcefield for atom C-839 with 2 bonds Can not find forcefield for atom C-840 with 3 bonds Can not find forcefield for atom C-841 with 3 bonds Can not find forcefield for atom C-842 with 2 bonds Can not find forcefield for atom C-843 with 2 bonds Could only find a forcefield type for 321 out of 843 atoms How to solve it ? Thanks in Advance -- 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] About Topology construction for CNT wrapped by Cyclic peptide
On Wed, Apr 10, 2013 at 8:56 AM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin , Thank you for your reply, I need to construct Topology For Carbon Nano tubes (CNT) in gromoff53a5.ff . For that When i run the Following Command ./g_x2top_d -f CNT.gro -o CNT.top -r CNT.rtp I have got Error as follows Can not find forcefield for atom N-325 with 0 bonds Can not find forcefield for atom CA-326 with 2 bonds Can not find forcefield for atom CB-327 with 2 bonds Can not find forcefield for atom CG-328 with 2 bonds Can not find forcefield for atom C-330 with 2 bonds Can not find forcefield for atom O-331 with 1 bonds Can not find forcefield for atom N-332 with 0 bonds The preceding lines appear to belong to a protein residue. Don't use g_x2top for proteins. That's what pdb2gmx is for. Can not find forcefield for atom C-836 with 3 bonds Can not find forcefield for atom C-837 with 3 bonds Can not find forcefield for atom C-838 with 2 bonds Can not find forcefield for atom C-839 with 2 bonds Can not find forcefield for atom C-840 with 3 bonds Can not find forcefield for atom C-841 with 3 bonds Can not find forcefield for atom C-842 with 2 bonds Can not find forcefield for atom C-843 with 2 bonds Could only find a forcefield type for 321 out of 843 atoms How to solve it ? You need a suitable .n2t file. For a CNT, it is trivial to create the necessary entry since the geometry is regular. Please consult the manual and website. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] atb topology files
hi, i want to ask which files should be selected when ligand topology is generated by prodrg server? and do they need also modification regards kalsoom -- 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] ligand topology error
hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that either: (1) the geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate what should i do this to remove the error? -- 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] ligand topology error
On 2/1/13 9:37 AM, az kalsom wrote: hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that either: (1) the geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate what should i do this to remove the error? Please read my previous reply to this same question. This is not the appropriate forum for such questions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] ligand topology
On 1/31/13 9:51 AM, az kalsom wrote: hi i have docked the compund with protein and selected the best protein-ligand conformation for simulations, but when i generate the topolgy for ligand by Automated Topology Builder (ATB) and Repository , job is killed every tym. error message is 1) geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate... what should i do to remove this ? There's clearly something wrong with your input, but since (1) we don't know what it is, (2) we don't know what you're doing, and (3) this forum isn't about ATB, it's pretty hard to help. Refer to the FAQ (http://compbio.biosci.uq.edu.au/atb/index.py?tab=faq_tab) and seek help from whatever resources ATB provides. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] drug topology file
On 1/30/13 3:27 PM, az kalsom wrote: hi, i wanted to know, what s simple way to correct the topology generated by PROGRG server i have read the paper mentioned in tutorial , but still i am nt able to correct the file please help me, should all CH3 CH2 charge ne made zero ? Not necessarily. Deriving parameters for the Gromos96 force fields is a somewhat ill-defined process, as iterative empirical refinements are often used. Building blocks of common functional groups are generally transferable between molecules, and recent papers have suggested parameters for many non-protein groups. There are probably a dozen or so papers that I would consider necessary reading before you should attempt to parameterize any molecule under Gromos96. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] protein topology file fetal error
hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SER 705 was not found in rtp entry SER with 10 atoms while sorting atoms.* PLEASE HELP ME IN REMOVING THIS ERROR WHAT SHOULD I DO TO REMOVE THIS ERROR ? REGARDS kalsoom -- 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] protein topology file fetal error
On 1/26/13 4:41 AM, az kalsom wrote: hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SER 705 was not found in rtp entry SER with 10 atoms while sorting atoms.* PLEASE HELP ME IN REMOVING THIS ERROR WHAT SHOULD I DO TO REMOVE THIS ERROR ? http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry You haven't said exactly what you're dealing with, but if you're trying to use a united-atom force field as in my tutorial, these force fields do not have explicit nonpolar hydrogen atoms. Adding -ignh to pdb2gmx is probably the solution. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] About topology for cyclic petide
Dear justin Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal But When I interactively Choose the Terminal By pdb2gmx It Shows Only 1)COO - 2)COOH 3)None I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide It Adds One Two oxygen atom on the Carbon Atom (O1 O2) . But I Need the Addition Of One Oxygen Atom How to Do It ? Which Database file Should I EDIT ? .C Terminal Data Base Thanks In Advance -- 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] About topology for cyclic petide
On 12/26/12 9:50 AM, vidhya sankar wrote: Dear justin Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal But When I interactively Choose the Terminal By pdb2gmx It Shows Only 1)COO - 2)COOH 3)None I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide It Adds One Two oxygen atom on the Carbon Atom (O1 O2) . But I Need the Addition Of One Oxygen Atom How to Do It ? It sounds like you made the wrong choice. The proper selection is None such that your C-terminus is treated like any internal residue and is engaged in a peptide bond with the N-terminus. The actual bond in this case is defined in specbond.dat since pdb2gmx can only otherwise handle linear sequences of residues. Which Database file Should I EDIT ? .C Terminal Data Base You don't need to edit anything, you only need to use the terminus selection mechanism correctly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] About topology construction for Cyclic peptide
On 17/09/2012 11:50 AM, vidhya sankar wrote: Dear Mark, Thank you for your reply I have used the peptide FLF For that pdb2gmx construct topology successfully with -ter choosing any thing for both terminal. OK, well you can work with that topology as your template for the same kind of procedure, but you will have to pay attention to the atom types of the N terminus of F (both N and its hydrogen atoms). They should match those of the N terminus of the C-terminal N in FXXXLF. But When i Choose none with -ter for both terminal It again shows error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. Shrug. You're not giving your pdb2gmx commands, any useful diagnostic output before the error message, or any information about the terminal residues, so you're making your own life hard by making every one's hard. Mark For your Convenience i have pasted the previous discussion That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? With Regards S.vidhyasankar -- 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] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations. However, in your tutorial you set all charges to zero with the same settings in the mdp file. Can you please make this clear for me? Should I use the topoly file with the original charges for both calculations? Thank you, Sonia Aguilera Graduate Student-Chemical Engineering Department Universidad de los Andes Colombia -- View this message in context: http://gromacs.5086.n6.nabble.com/Topology-and-mdp-file-for-coupling-vdw-and-coulombic-interactions-for-running-FE-calculations-using-R-tp5001021p5001043.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
On 9/17/12 3:38 PM, Sonia Aguilera wrote: Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations. However, in your tutorial you set all charges to zero with the same settings in the mdp file. Can you please make this clear for me? Should I use the topoly file with the original charges for both calculations? Yes, the topology can be complete with charges. They were zeroed out in the tutorial because (1) those were the files provided with an old Gromacs tutorial (for version 3.3.1) and (2) it was conceptually easier. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] About topology construction for yclic pepetide
Dear Mark , Again Thanks for you reply After Editing my pdb file from intial FL to FLF format Then i Run pdb2gmx for my linaer pdb file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to Rectify this error For your Remembrance i pasted your previous Discussion 1) Take your initial coordinate file, make a copy and in it make a copy of the first residue and place it after the last residue, taking care to obey the format of the file you're using, and update things like atom counts and atom and residue indices. The coordinates of the copied atoms don't matter. Now you have a coordinate file for FLF. 2) Process that with pdb2gmx using -ter and choosing none. This has built a linear topology for FLF, with a correct L-to-F link for you to use as a template for making a cyclic FL. Thanks in Advance -- 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] About topology construction for yclic pepetide
On 17/09/2012 2:55 AM, vidhya sankar wrote: Dear Mark , AgainThanks for you reply After Editing my pdb file from intial FL to FLF format Then i Run pdb2gmx for my linaerpdb file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to Rectify this error That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? Mark For your Remembrance i pasted your previous Discussion 1) Take your initial coordinate file, make a copy and in it make a copy of the first residue and place it after the last residue, taking care to obey the format of the file you're using, and update things like atom counts and atom and residue indices. The coordinates of the copied atoms don't matter. Now you have a coordinate file for FLF. 2) Process that with pdb2gmx using -ter and choosing none. This has built a linear topology for FLF, with a correct L-to-F link for you to use as a template for making a cyclic FL. Thanks in Advance -- 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] About topology construction for Cyclic peptide
Dear Mark, Thank you for your reply I have used the peptide FLF For that pdb2gmx construct topology successfully with -ter choosing any thing for both terminal. But When i Choose none with -ter for both terminal It again shows error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For your Convenience i have pasted the previous discussion That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? With Regards S.vidhyasankar -- 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] create topology other solvent
Dear all users, I had this problem and i dont know how to solve it.I need to create other co-solvent which does not have in pdb bank. I to optimize it by using GAMESS software and do RESP for charge calculation.When i do all this part there some error happened and I manage to solve that part. Unfortunately there are no coordinate that create. I have been told to do it by using amber for charge calculation before can use it in gromacs. Any suggestion to produce this cosolvent with pdb format? Thanks. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. 013-7188131 alternative email : syafiqahabdulgh...@gmail.com -- 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] create topology other solvent
On 11/09/2012 1:33 PM, Nur Syafiqah Abdul Ghani wrote: Dear all users, I had this problem and i dont know how to solve it.I need to create other co-solvent which does not have in pdb bank. I to optimize it by using GAMESS software and do RESP for charge calculation.When i do all this part there some error happened and I manage to solve that part. Unfortunately there are no coordinate that create. I have been told to do it by using amber for charge calculation before can use it in gromacs. Any suggestion to produce this cosolvent with pdb format? https://www.google.com.au/search?q=gromacs+mixed+solvent ;-) 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] Re: Topology file
Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp #include topol_Protein_chain_G.itp ;Include ligand topology #include FDP_Dp.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Topology file
On 8/15/12 9:12 AM, Ankita naithani wrote: Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? Yes, #include statements for position restraint files are contained in each chain topology. -Justin On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp #include topol_Protein_chain_G.itp ;Include ligand topology #include FDP_Dp.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ions topology
Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before I can begin with my simulations. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ions topology
On 14/08/2012 7:45 PM, Ankita naithani wrote: Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before I can begin with my simulations. Availability depends on the force field, so start looking in its files distributed by GROMACS. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ions topology
Dear Mark, Thank you for your reply. I am using gromos53a6 force field. On Tue, Aug 14, 2012 at 11:16 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/08/2012 7:45 PM, Ankita naithani wrote: Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before I can begin with my simulations. Availability depends on the force field, so start looking in its files distributed by GROMACS. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 topology error.
DEar all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Topology include file ion.itp not found Suryanarayana Seera, PhD student, Hyderabad, India. -- 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 topology error.
On 5/17/12 7:05 AM, Seera Suryanarayana wrote: DEar all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Topology include file ion.itp not found The name of the file is ions.itp not ion.itp. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] CHARMM27 topology for DOPC
Hi GMX Users, I have generated a topology entry for the DOPC lipid for charmm27.ff/lipids.rtp by copying and editing the entry of POPC. My DOPC has passed two simple tests with gromacs-4.5.3 on a test structure of an isolated model molecule (generated with CHARMM) 1) energy minimization produced a reasonable structure close to starting coordinates 2) all energy components agreed with CHARMM v. 27 results to at least 4 digits. I enclose my topology file; I would welcome - information about other DOPC topologies in GMX - critical comments - suggestions for more simple tests ( the 100 ns solvated bilayer simulation is already on my list) Greetings Krzysztof Kuczera -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html [ DOPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 H52 HAL20.0918 P1 PL 1.5019 O3 O2L -0.78 20 O4 O2L -0.78 21 O1 OSL -0.57 22 O2 OSL -0.57 23 C1 CTL2-0.08 24 HA HAL20.0925 HB HAL20.0926 C2 CTL10.0427 HS HAL10.0928 O21 OSL -0.34 29 C21 CL 0.6330 O22 OBL -0.52 31 C22 CTL2-0.08 32 H2R HAL20.0933 H2S HAL20.0934 C3 CTL2-0.05 35 HX HAL20.0936 HY HAL20.0937 O31 OSL -0.34 38 C31 CL 0.6339 O32 OBL -0.52 40 C32 CTL2-0.08 41 H2X HAL20.0942 H2Y HAL20.0943 C23 CTL2-0.18 44 H3R HAL20.0945 H3S HAL20.0946 C24 CTL2-0.18 47 H4R HAL20.0948 H4S HAL20.0949 C25 CTL2-0.18 50 H5R HAL20.0951 H5S HAL20.0952 C26 CTL2-0.18 53 H6R HAL20.0954 H6S HAL20.0955 C27 CTL2-0.18 56 H7R HAL20.0957 H7S HAL20.0958 C28 CTL2-0.18 59 H8R HAL20.0960 H8S HAL20.0961 C29 CEL1-0.15 62 H91 HEL10.1563 C210CEL1-0.15 64 H101HEL10.1565 C211CTL2-0.18 66 H11RHAL20.0967 H11SHAL20.0968 C212CTL2-0.18 69 H12RHAL20.0970 H12SHAL20.0971 C213CTL2-0.18 72 H13RHAL20.0973 H13SHAL20.0974 C214CTL2-0.18 75 H14RHAL20.0976 H14SHAL20.0977 C215CTL2-0.18 78 H15RHAL20.0979 H15SHAL20.0980 C216CTL2-0.18 81 H16RHAL20.0982 H16SHAL20.0983 C217CTL2-0.18 84 H17RHAL20.0985 H17SHAL20.0986 C218CTL3-0.27 87 H18RHAL30.0988 H18SHAL30.0989 H18THAL30.0990 C33 CTL2-0.18 91 H3X HAL20.0992 H3Y HAL20.0993 C34 CTL2-0.18 94 H4X HAL20.0995 H4Y HAL20.0996 C35 CTL2-0.18 97 H5X HAL20.0998 H5Y HAL20.0999 C36 CTL2-0.18 100 H6X HAL20.09101 H6Y HAL20.09102 C37 CTL2-0.18 103 H7X HAL20.09104 H7Y HAL20.09105 C38 CTL2-0.18 106 H8X HAL20.09107 H8Y HAL20.09108 C39 CEL1-0.15 109 H92 HEL10.15110 C310CEL1-0.15 111 H102HEL10.15112 C311CTL2-0.18 113 H11XHAL20.09114 H11Y
Re: [gmx-users] CHARMM27 topology for DOPC
Compare and contrast with Klauda et al. Phys Chem. B, 2010, 114, 7830 ? On 2012-03-23 02:28:45PM -0500, Krzysztof Kuczera wrote: Hi GMX Users, I have generated a topology entry for the DOPC lipid for charmm27.ff/lipids.rtp by copying and editing the entry of POPC. My DOPC has passed two simple tests with gromacs-4.5.3 on a test structure of an isolated model molecule (generated with CHARMM) 1) energy minimization produced a reasonable structure close to starting coordinates 2) all energy components agreed with CHARMM v. 27 results to at least 4 digits. I enclose my topology file; I would welcome - information about other DOPC topologies in GMX - critical comments - suggestions for more simple tests ( the 100 ns solvated bilayer simulation is already on my list) Greetings Krzysztof Kuczera -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html [ DOPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 H52 HAL20.0918 P1 PL 1.5019 O3 O2L -0.78 20 O4 O2L -0.78 21 O1 OSL -0.57 22 O2 OSL -0.57 23 C1 CTL2-0.08 24 HA HAL20.0925 HB HAL20.0926 C2 CTL10.0427 HS HAL10.0928 O21 OSL -0.34 29 C21 CL 0.6330 O22 OBL -0.52 31 C22 CTL2-0.08 32 H2R HAL20.0933 H2S HAL20.0934 C3 CTL2-0.05 35 HX HAL20.0936 HY HAL20.0937 O31 OSL -0.34 38 C31 CL 0.6339 O32 OBL -0.52 40 C32 CTL2-0.08 41 H2X HAL20.0942 H2Y HAL20.0943 C23 CTL2-0.18 44 H3R HAL20.0945 H3S HAL20.0946 C24 CTL2-0.18 47 H4R HAL20.0948 H4S HAL20.0949 C25 CTL2-0.18 50 H5R HAL20.0951 H5S HAL20.0952 C26 CTL2-0.18 53 H6R HAL20.0954 H6S HAL20.0955 C27 CTL2-0.18 56 H7R HAL20.0957 H7S HAL20.0958 C28 CTL2-0.18 59 H8R HAL20.0960 H8S HAL20.0961 C29 CEL1-0.15 62 H91 HEL10.1563 C210CEL1-0.15 64 H101HEL10.1565 C211CTL2-0.18 66 H11RHAL20.0967 H11SHAL20.0968 C212CTL2-0.18 69 H12RHAL20.0970 H12SHAL20.0971 C213CTL2-0.18 72 H13RHAL20.0973 H13SHAL20.0974 C214CTL2-0.18 75 H14RHAL20.0976 H14SHAL20.0977 C215CTL2-0.18 78 H15RHAL20.0979 H15SHAL20.0980 C216CTL2-0.18 81 H16RHAL20.0982 H16SHAL20.0983 C217CTL2-0.18 84 H17RHAL20.0985 H17SHAL20.0986 C218CTL3-0.27 87 H18RHAL30.0988 H18SHAL30.0989 H18THAL30.0990 C33 CTL2-0.18 91 H3X HAL20.0992 H3Y HAL20.0993 C34 CTL2-0.18 94 H4X HAL20.0995 H4Y HAL20.0996 C35 CTL2-0.18 97 H5X HAL20.0998 H5Y HAL20.0999 C36 CTL2-0.18 100 H6X HAL20.09101 H6Y HAL20.09102 C37 CTL2-0.18 103 H7X HAL20.09104 H7Y HAL20.09105 C38 CTL2-0.18 106 H8X HAL20.09107 H8Y HAL20.09108 C39 CEL1-0.15 109 H92 HEL10.15110 C310CEL1-0.15 111 H102HEL10.15112 C311CTL2-0.18 113
[gmx-users] Generating topology
Hi A protein sits on the top of another protein (not docking). I then used pdb2gmx command to generate the topology. Surprisingly, i got five files, as given below: I think the two proteins are not connected each other. is it possible to make it one posre and topol file. Many thanks in advance posre_Protein_chain_A.itp posre_Protein_chain_A2.itp topol.top topol_Protein_chain_A.itp topol_Protein_chain_A2.itp -- 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] Generating topology
On Thu, Mar 22, 2012 at 11:54 AM, Spring buds winterho...@gmail.com wrote: Hi A protein sits on the top of another protein (not docking). I then used pdb2gmx command to generate the topology. Surprisingly, i got five files, as given below: I think the two proteins are not connected each other. is it possible to make it one posre and topol file. You have already have one posre and topol.top more topol.top check what's inside your topol.top. pay attention to include Many thanks in advance posre_Protein_chain_A.itp posre_Protein_chain_A2.itp topol.top topol_Protein_chain_A.itp topol_Protein_chain_A2.itp -- 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 -- 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] Generating topology
On 22/03/2012 2:54 PM, Spring buds wrote: Hi A protein sits on the top of another protein (not docking). I then used pdb2gmx command to generate the topology. Surprisingly, i got five files, as given below: I think the two proteins are not connected each other. is it possible to make it one posre and topol file. Yes, see discussion in pdb2gmx -h. (Checking -h should always been a first place to look for information) Mark Many thanks in advance posre_Protein_chain_A.itp posre_Protein_chain_A2.itp topol.top topol_Protein_chain_A.itp topol_Protein_chain_A2.itp -- 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] opls topology for butanol, hexanol, heptanol
Hi, I am looking for opls topology files for butanol, hexanol, and heptonal. I have been using opls itp for methanol, ethanol and propanol which are available with the gromacs package, but itp for longer alcohol are not available. I have the following two question. Where could I find those parameters? If I need to construct them myself, where could I get started? Thank you. Regards, Zhuyi -- 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] opls topology for butanol, hexanol, heptanol
Zhuyi Xue wrote: Hi, I am looking for opls topology files for butanol, hexanol, and heptonal. I have been using opls itp for methanol, ethanol and propanol which are available with the gromacs package, but itp for longer alcohol are not available. I have the following two question. Where could I find those parameters? If I need to construct them myself, where could I get started? Extension of smaller alcohols by simple CH2 and CH3 groups is reasonably easy since the charges and atom types are not connected to chain length. In general, refer to the OPLS parameterization papers for the exact methods for charge derivation and atom type implementation. The methods are quite well explained in these papers. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] HEME topology
Anik Sen wrote: Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ PRODRG will be unable to handle this type of molecule, since it contains iron. What's more, PRODRG topologies are generally incorrect for even the simplest molecules. Several of the force fields in Gromacs contain heme parameters, otherwise they can be found in the literature. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal Prasad [nimmynir...@gmail.com] *Sent:* Wednesday, January 11, 2012 9:45 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] HEME topology Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] HEME topology
Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- 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] HEME topology
Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal Prasad [nimmynir...@gmail.com] Sent: Wednesday, January 11, 2012 9:45 AM To: Discussion list for GROMACS users Subject: [gmx-users] HEME topology Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- 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] Re: topology file
On 2011-12-24 13:08, Su Nh wrote: Dear Prof. van der Spoe Thank you for your responce. But I want to know if the charges in the topology files, which are built by ATB, are accurate and there is no need to re-calculate them or not? On the oder hand, what is the compatible parameters (basis set and method) with GROMOS force field? Thank you very much indeed su Ask the guys who made the website please. You can also check out http://virtualchemistry.org for OPLS GAFF. Please put further questions on the mailing list. -- 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
[gmx-users] regarding topology
hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh it showed error as *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 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 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'BFC' not found in residue topology database* i know i want to include BFC residue into my rtp file but dono how to include.. how can i get those parameter to include like its angles, dihedrals etc. x2top ll give top and rtp file.so i tried that. how to solve my problem. help me with your answer sir. -- 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 topology
priya thiyagarajan wrote: hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh it showed error as *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 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 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'BFC' not found in residue topology database* i know i want to include BFC residue into my rtp file but dono how to include.. how can i get those parameter to include like its angles, dihedrals etc. x2top ll give top and rtp file.so i tried that. how to solve my problem. help me with your answer sir. Start with the link I already provided and follow the instructions exactly: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Doing so will require a suitable .rtp entry (see the manual), which may also require you to derive parameters for the species of interest, an expert topic that may take considerable time to achieve. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Generating topology file
Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- 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] Generating topology file
I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg. A hack would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges. Good luck, Alan On 23 November 2011 10:35, madhumita das madhumita.bioi...@gmail.comwrote: Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] Ligand topology in topol.top
Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? Regards, Steven -- 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] Ligand topology in topol.top
Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Ligand topology in topol.top
On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Steven -- 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] Ligand topology in topol.top
Steven Neumann wrote: On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Then the position restraints are not being applied to the ligand. They can't be. Once the protein [moleculetype] is introduced, all [position_restraints] directives immediately after are applied to it. Try invoking the restraints separately, i.e. with define = -DPOSRES -DPOSRES_LIGAND and you will get a fatal error. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Ligand topology in topol.top
On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include ligand.itp ; Ligand position restraints #ifdef POSRES #include posre_ligand.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp When I wanted to run NVT I obtained: Fatal error: Syntax error - File egcg.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes However when I included my topology as: ; Include forcefield parameters #include charmm27.ff/forcefield.itp #include ligand.itp [ moleculetype ] ; Name nrexc .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_egcg.itp #endif ; Include water topology #include charmm27.ff/tip3p.itp Everything seems to be ok! Any clue why is that? The topology must follow a defined order. Please consult Chapter 5 of the manual for the required hierarchy. Of course, the latter case will also not work, because you've introduced ligand position restraints after the protein [moleculetype], so if invoked, they will cause a different fatal error. The Gromacs site also has more on these types of errors, as well as the list archive, where this error has been posted and solved hundreds of times. -Justin Thank you Justin! But actually the last case I provided actually works... Then the position restraints are not being applied to the ligand. They can't be. Once the protein [moleculetype] is introduced, all [position_restraints] directives immediately after are applied to it. Try invoking the restraints separately, i.e. with define = -DPOSRES -DPOSRES_LIGAND and you will get a fatal error. -Justin You are as always right :) Thanks! Steven -- 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] Re: topology error
only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also. I used gromas96 43a1 force field. I found following error when i was doing grompp for energy minimization. I went through FAQ and checked all but i couldn't find what exactly it was. So, I attached that files to you. I need your help to solve this Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 377 Fatal error: number of coordinates in coordinate file (GR_b4ion.gro, 66074) does not match topology (GR.top, 66015) -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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] error_in topology
Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (1AKI_solv.gro, 4164) does not match topology (topol.top, 5527) I used the following lines to do that pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em in the grompp it says the error , how to solve this , and it comes only for tip4p not for other water models. thanks in advance 1AKI.pdb Description: application/aportisdoc -- 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] error_in topology
balaji nagarajan wrote: Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (1AKI_solv.gro, 4164) does not match topology (topol.top, 5527) I used the following lines to do that pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top You told pdb2gmx to write the TIP4P topology into your .top, but then you used a 3-point water model. You need to solvate with tip4p.gro. -Justin grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em in the grompp it says the error , how to solve this , and it comes only for tip4p not for other water models. thanks in advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: topology error
On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA ithayar...@gmail.com wrote: only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also. I used gromas96 43a1 force field. I found following error when i was doing grompp for energy minimization. I went through FAQ and checked all but i couldn't find what exactly it was. So, I attached that files to you. I need your help to solve this Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 377 Fatal error: number of coordinates in coordinate file (GR_b4ion.gro, 66074) does not match topology (GR.top, 66015) I used to count the atom numbers in .gro file and manually modify the topology to make them match. -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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] Creating topology with bonds over pbc
Hi all, Let's say I created a pdb of a B-DNA Double-Helix with amber tools. Now I would like to have a topology in which the last residues are bonded to the first. How can I do that expect of actually mess together a topology file by self written scripts and/or handwork? Also if create helix strings without substituting the terminal phosphate pdb2gmx doesn't seem to accept it. Thanks for any hints, W.Müller -- 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] Creating topology with bonds over pbc
On 4/10/2011 6:25 PM, Wojciech Müller wrote: Hi all, Let's say I created a pdb of a B-DNA Double-Helix with amber tools. Now I would like to have a topology in which the last residues are bonded to the first. How can I do that expect of actually mess together a topology file by self written scripts and/or handwork? I've never done anything like it, but I would guess that you can * generate with AMBER tools an equivalent non-periodic structure with suitable termini (you need the ordering of the atoms belonging to non-terminal monomers to match the ordering of your structure above), * use pdb2gmx on that, * take the top file and remove the atoms for the termini, and the intra-termini bonds, * create the head-to-tail [ bonds ] in the .top file, and * match that with your structure above for grompp. Sounds like about 15 minutes' work, if you already know the .top file format and how to use AMBER tools. Mark Also if create helix strings without substituting the terminal phosphate pdb2gmx doesn't seem to accept it. Thanks for any hints, W.Müller -- 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] Arginine_Hydrochloride topology
I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Arginine_Hydrochloride topology
shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Arginine_Hydrochloride topology
I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box shahid nayeem On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/**Documentation/How-tos/**Multiple_Chainshttp://www.gromacs.org/Documentation/How-tos/Multiple_Chains . Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
Re: [gmx-users] Arginine_Hydrochloride topology
shahid nayeem wrote: I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box What is in protein.pdb? I don't believe genbox can handle multi-residue molecules, but I could be wrong. Or there could be insufficient space, which is quite likely. A 1.8-nm box is too small for all but the tiniest proteins. The better approach: 1. Run pdb2gmx on protein.pdb 2. Run pdb2gmx on arg.pdb, convert the .top to .itp and #include it in the .top from (1) 3. Run genbox -ci to add arg.gro molecules into the system -Justin shahid nayeem On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.__au mailto:mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/__Documentation/How-tos/__Multiple_Chains http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Arginine_Hydrochloride topology
Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Arginine_Hydrochloride topology
On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] PRODRG topology
Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? Thank you in advance, Jan -- 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] PRODRG topology
Marzinek, Jan wrote: Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? The Gromos96 force fields are united-atom force fields and may not use all the H atoms your input coordinates did. If you suspect some issue with protonation state, PRODRG can be forced into certain protonation with the ADDHYD or DELHYD keywords. Be advised, of course, of the usual caveats regarding the quality of PRODRG topologies: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Arginine_Hydrochloride topology
shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Arginine_Hydrochloride topology
Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. shahid Nayeem -- 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] required topology stuff modification for GBSA
Dear GROMACS users: This is self-reply to resolve the following error I'd met. Then I believe the error Fatal error: Cannot find length for atoms 1-3 involved in angle. occurs with some side-effects from the implicit solvent setting. I'd found that the topology stuff should be more strictly written with implicit_solvent=GBSA than that with implicit_solvent=no. For simple example, all-atom CH4 molecule has five atoms and four bonds and six angles. If I only have five angles by mistake, it is tolerant with implicit_solvent=no but result in the error above with implicit_solvent=GBSA. It means you should check the number of angles, if you've got the error when you change implicit_solvent=no to implicit_solvent=GBSA. Hope it helps. Regards, Makoto Yoneya, Dr. http://staff.aist.go.jp/makoto-yoneya/ -- 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] missing topology file adn creating a new one
Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topol.top -ff select* when it prompts for a force field i selected charmm27 which is what i used for the simulation it give me the following error Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) --- Program g_x2top, VERSION 4.5.3 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for charmm27.ff) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors i* tried to use pdb2gmx as well pdb2gmx -f 2.pdb -o 2.gro -p topool.top * End terminus GLU-56: COO- Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/rna.arn Checking for duplicate atoms Now there are 16 residues with 247 atoms Chain time... Making bonds... Number of bonds was 250, now 250 Generating angles, dihedrals and pairs... Before cleaning: 649 pairs Before cleaning: 654 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 14 cmap torsion pairs There are 654 dihedrals, 35 impropers, 444 angles 640 pairs, 250 bonds and 0 virtual sites Total mass 1860.928 a.m.u. Total charge -3.000 e Writing topology Processing chain 2 (3 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue NA2139 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2140 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2141 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 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'NA' 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 -- 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] missing topology file adn creating a new one
sreelakshmi ramesh wrote: Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topol.top -ff select* when it prompts for a force field i selected charmm27 which is what i used for the simulation it give me the following error Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) Reading file beta_md17.tpr, VERSION 4.5.3 (single precision) --- Program g_x2top, VERSION 4.5.3 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for charmm27.ff) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors i* tried to use pdb2gmx as well pdb2gmx -f 2.pdb -o 2.gro -p topool.top * End terminus GLU-56: COO- Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /sw/gromacs-4.5.3/share/gromacs/top/charmm27.ff/rna.arn Checking for duplicate atoms Now there are 16 residues with 247 atoms Chain time... Making bonds... Number of bonds was 250, now 250 Generating angles, dihedrals and pairs... Before cleaning: 649 pairs Before cleaning: 654 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 14 cmap torsion pairs There are 654 dihedrals, 35 impropers, 444 angles 640 pairs, 250 bonds and 0 virtual sites Total mass 1860.928 a.m.u. Total charge -3.000 e Writing topology Processing chain 2 (3 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue NA2139 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2140 in chain not identified as Protein/RNA/DNA. Warning: Starting residue NA2141 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 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'NA' 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 pdb2gmx is ill-suited for dealing with multiple molecules. You haven't said what's in your system, but if it's something simple like a protein in water with ions, it's trivial to re-create a topology. Just run pdb2gmx on the protein only, then manually add the missing water and ions to the topology. If you're system is something more complex than that, then hopefully you've documented your procedure well such that you can reproduce it. And don't let files go missing :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] required topology stuff modification for GBSA
On 06/24/2011 02:21 PM, Makoto Yoneya wrote: Dear GROMACS experts: I'd tried to use a GBSA implicit solvent function in ver. 4.5.4. I'd convinced the normal run with vacuo with simply high epsilon_r setting. After that, I'd modified the topology stuff by adding [ implicit_genborn_params ] entry and then implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 in the mdp file to try a GBSA implicit solvent run. Then I'd suffer error from grompp like as Fatal error: Cannot find length for atoms 1-3 involved in angle. Actually, there is no covalent bond between 1-3 (there is an angle with atoms 1-2-3, but these are bonded only with 1-2 and 2-3). You don't say what your force field is, but those symptoms are suggestive of a problem with CHARMM force field lacking Urey-Bradley interaction parameters for atoms 1-2-3. If so, this is not a GB problem per se. Mark I'm wondering what kinds of extra-modification in topology stuff besides adding [ implicit_genborn_params ] entry for the implicit solvent runs from the runs without it. Any info. will be welcome. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN http://staff.aist.go.jp/makoto-yoneya/ -- 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] required topology stuff modification for GBSA
Dear Mark: Thank you for your comment. You don't say what your force field is, but those symptoms are suggestive of a problem with CHARMM force field lacking Urey-Bradley interaction parameters for atoms 1-2-3. If so, this is not a GB problem per se. Mark Sorry for the lack of info. The force field was general AMBER and the topology file was basically generated using the utility ACPYPE. And as I wrote, I'd convinced the normal run with vacuo with simply high epsilon_r setting. The corresponding runs with implicit_solvent = NO result in no errors. Then I believe the error Fatal error: Cannot find length for atoms 1-3 involved in angle. occurs with some side-effects from the implicit solvent setting. Also I found the same error reports on the gmx-user archive (although no info. For solve it). It suggest the error would be a general one. Thanks anyway. Regards. -- 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] creating topology using g_x2top
Dear all , I want to simulate a double walled nano tube in spc water i had made the pdb file now if i use g_x2top for creating the topology file it gives me the following error . Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa* it gives the following error *Can not find forcefield for atom OW-5432 with 2 bonds Can not find forcefield for atom OW-5435 with 2 bonds Can not find forcefield for atom OW-5438 with 2 bonds Can not find forcefield for atom OW-5441 with 2 bonds Can not find forcefield for atom OW-5444 with 2 bonds Can not find forcefield for atom OW-5447 with 2 bonds Can not find forcefield for atom OW-5450 with 2 bonds looking forward for your suggestions, Thanks in advance, sree.* -- 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] creating topology using g_x2top
sreelakshmi ramesh wrote: Dear all , I want to simulate a double walled nano tube in spc water i had made the pdb file now if i use g_x2top for creating the topology file it gives me the following error . Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa* it gives the following error *Can not find forcefield for atom OW-5432 with 2 bonds Can not find forcefield for atom OW-5435 with 2 bonds Can not find forcefield for atom OW-5438 with 2 bonds Can not find forcefield for atom OW-5441 with 2 bonds Can not find forcefield for atom OW-5444 with 2 bonds Can not find forcefield for atom OW-5447 with 2 bonds Can not find forcefield for atom OW-5450 with 2 bonds Presumably you have water in your starting structure. Don't run g_x2top on configurations with multiple molecules. Run the command on your CNT and nothing else, then proceed to solvate and simply #include the .itp file for your desired water model in the .top. -Justin looking forward for your suggestions, Thanks in advance, sree.* -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] recovering topology
Hi gmx-users: Is it possible to recover the topology from cpt file, it is so.. how and what command i need to use? Thanks Rama -- 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] recovering topology
On 18/05/2011 4:34 PM, Ramachandran G wrote: Hi gmx-users: Is it possible to recover the topology from cpt file, it is so.. how and what command i need to use? No, it is not stored there. It can be found only in .itp/.top/.tpr files, in various forms. 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
Re: [gmx-users] recovering topology
Hey Rama, I've lost my topology before, so I've used pdb2gmx to make new ones if I had the .gro file. Also I think that command can use an input .tpr file as well. Maybe that would help, Taylor --- On Tue, 5/17/11, Ramachandran G gtr...@gmail.com wrote: From: Ramachandran G gtr...@gmail.com Subject: [gmx-users] recovering topology To: gmx-users@gromacs.org Date: Tuesday, May 17, 2011, 11:34 PM Hi gmx-users: Is it possible to recover the topology from cpt file, it is so.. how and what command i need to use? Thanks Rama -Inline Attachment Follows- -- 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-- 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] CNT topology
Dear All Users I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by VMD and then made .gro by editconf -f file.pdb -o file.gro -box 4 command. then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by x2top -f file.gro -o topol.top -ff cnt_oplsaa -name CNT -noparam -pbc command. it makes topology file. but when I want to add water by genbox it make topology.top but there is not the water parameters(there is only number of water molecules at the end of file). then I use #include command for tip3p.itp model. when I want do em run by grompp, it dos not make .tpr and give error: Fatal error: [ file tip3p,itp, Line 42 ]: Atom index (1) in settles out of bounds (1-0). . I studied some guides to another gromacs user in mailing list and add #define ff.. in ffcnt_oplsaa.itp but it gives this error again. I think because of use ffcnt_oplsaa.itp , it can't include tip3p.itp. but when I add this forcefield to tip3p.itp by hand this error again comes. please guide me. thank you so much Best Sara Azhari Phd Student -- 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
