[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
