Re: [gmx-users] Helicity
I am not sure if I can give you the most adequate answer because I am not in a computer with GROMACS right now. I think that the easiest way to do that is by using the do_dssp command which gives you the number of residues in helix, b-sheet, etc, over time and then do the average of the corresponding column. Regards, Diogo shivangi nangia shivangi.nan...@gmail.com escreveu no dia Fri Feb 06 2015 at 20:42:52: Thanks. I am aware of all those commands. My question is specific to gromacs out, the file helicity.xvg has an output of the form: 9 @title Helicity per Residue 10 @xaxis label Residue 11 @yaxis label % of time 12 @TYPE xy 13 1 0 14 2 92.6148 15 3 86.8263 16 4 96.008 ..so on It is telling me residue 2 is 92 % of time (that I specified) helical. I want the average helicity of the peptide during the specified time. Thanks, sxn On Fri, Feb 6, 2015 at 3:11 PM, Diogo Vila Viçosa diogo.vic...@fc.ul.pt wrote: I Shivangi, There are several ways to calculate the average helicity. If you are using linux you can easily do that with a simple awk / bash script. In windows you can paste the number of residues in helical structure over time in an excel spreadsheet and calculate the average, etc.. I suppose you are using linux and my advice to you is: try to learn something about awk, sed, bash, etc... before you dive in into more complex things such as a MD simulation. Best regards, Diogo Vila Viçosa shivangi nangia shivangi.nan...@gmail.com escreveu no dia Fri Feb 06 2015 at 20:00:41: Hello gmx-users, I want to calculate the average helicity of a peptide in last 20 ns of the simulation. g_helix is giving % helicity per residue during the specified period of time. Is there a way to do what I wish to calculate. Kindly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Helicity
I Shivangi, There are several ways to calculate the average helicity. If you are using linux you can easily do that with a simple awk / bash script. In windows you can paste the number of residues in helical structure over time in an excel spreadsheet and calculate the average, etc.. I suppose you are using linux and my advice to you is: try to learn something about awk, sed, bash, etc... before you dive in into more complex things such as a MD simulation. Best regards, Diogo Vila Viçosa shivangi nangia shivangi.nan...@gmail.com escreveu no dia Fri Feb 06 2015 at 20:00:41: Hello gmx-users, I want to calculate the average helicity of a peptide in last 20 ns of the simulation. g_helix is giving % helicity per residue during the specified period of time. Is there a way to do what I wish to calculate. Kindly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] A quick question regarding topology generation
Dear Users During topology generation many a times we clean the PDB file by stripping it off waters ( crystallized ) or some other small molecules ( like a small ligand ) etc , which are of no immediate interest , as we concentrate on getting the structure for the protein ( biomolecule ) upon which we want to perform molecular dynamics. My question is will that create any distortion on the protein structure generated by pdb2gmx? One of my colleagues told me that the other atoms like those of the water and the small ligands may be participating in hydrogen bonds with the protein which can stabilize the structure. So if I remove them then I am making the protein structure unstable. I told him that I do energy minimization after solvation to stabilize my structure but he is saying that it is unstable since the beginning. I know that I can use RMSD , DSSP to validate the structure but still I am not able to figure out an answer to his question. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] A quick question regarding topology generation
On 2/6/15 3:37 PM, Agnivo Gosai wrote: Dear Users During topology generation many a times we clean the PDB file by stripping it off waters ( crystallized ) or some other small molecules ( like a small ligand ) etc , which are of no immediate interest , as we concentrate on getting the structure for the protein ( biomolecule ) upon which we want to perform molecular dynamics. My question is will that create any distortion on the protein structure generated by pdb2gmx? One of my colleagues told me that the other atoms like those of the water and the small ligands may be participating in hydrogen bonds with the protein which can stabilize the structure. So if I remove them then I am making the protein structure unstable. I told him that I do energy minimization after solvation to stabilize my structure but he is saying that it is unstable since the beginning. If the crystal waters or ligands are structurally or functionally important, they can have an effect. Waters on the surface of the protein probably don't matter at all (in most cases), but waters in the active/binding site may be significant, though if their removal causes some massive distortion in the structure, I'd be suspect about a lot more before I'd blame water. Proper equilibration with restraints on the protein, allowing water to soak into available volume, will probably alleviate most issues you might encounter. Rushing the equilibration could negatively impact the outcome. Ligand binding can induce significant conformational change. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Helicity
On 2/6/15 3:42 PM, shivangi nangia wrote: Thanks. I am aware of all those commands. My question is specific to gromacs out, the file helicity.xvg has an output of the form: 9 @title Helicity per Residue 10 @xaxis label Residue 11 @yaxis label % of time 12 @TYPE xy 13 1 0 14 2 92.6148 15 3 86.8263 16 4 96.008 ..so on It is telling me residue 2 is 92 % of time (that I specified) helical. I want the average helicity of the peptide during the specified time. The proper tool for this is do_dssp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Distance restraint between two chains' com
On 2/6/15 8:47 AM, WT Ren wrote: Dear Justin: Sorry to bother you again When I did a long flat-bottom distance restraint(about 2nm), I got the error message: “There is no domain decomposition for 8 nodes” So is there any way to do a long distance restraint properly. Restraints limit DD cell size, so you're limited to fewer DD cells or not using DD at all (OpenMP only). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Covalent bond/crosslink formation with calcium
On 2/6/15 10:44 AM, Turgay Cakmak wrote: Thank you for the swift reply! We have decided against defining covalent bonds and went with the calcium-within-peptide-fiber configuration, but we have run into another problem, in that some of the calcium cations vanish from the unit cell that the fiber is in, and appear in the next unit cell, when we run an energy minimization. The missing cations are all on the same side of the peptide fiber and form a neat half-cylinder on the adjecent unit cell, so we are fairly certain that the problem has to do with our box definition. However, the entire structure is within our dodecahedral box prior to energy optimization. Is there any reason that the calciums would change position after energy minimization? Do we have to redefine our box afterwards? Without seeing the actual commands used to set this up and post-process with trjconv, and probably some images of before and after, it's hard to be specific. Sounds like a normal consequence of periodicity and possibly incorrect unwrapping via trjconv. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx question - protonation
Dear Users I am using the default settings for the pdb2gmx program and I leave the protonation of AA residues to the program. Can anybody tell me about the default protonation states of LYS, ASP, GLU, CYS or HIS employed by pdb2gmx ? I checked the manual but it is not explicitly mentioned. Is there any literature available. I am sorry if I am asking for too much. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx question - protonation
On 2/6/15 9:29 PM, Agnivo Gosai wrote: Dear Users I am using the default settings for the pdb2gmx program and I leave the protonation of AA residues to the program. Can anybody tell me about the default protonation states of LYS, ASP, GLU, CYS or HIS employed by pdb2gmx ? I checked the manual but it is not explicitly mentioned. Is there any literature available. I am sorry if I am asking for too much. It is explained by reading pdb2gmx -h. The default protonation states for all titratable residues are listed. Histidine protonation is determined by proximity of groups that can participate in hydrogen bonding. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Distance restraint between two chains' com
Dear Justin: Thanks for your reply What a pity! Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn* On Sat, Feb 7, 2015 at 5:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/6/15 8:47 AM, WT Ren wrote: Dear Justin: Sorry to bother you again When I did a long flat-bottom distance restraint(about 2nm), I got the error message: “There is no domain decomposition for 8 nodes” So is there any way to do a long distance restraint properly. Restraints limit DD cell size, so you're limited to fewer DD cells or not using DD at all (OpenMP only). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Helicity
Hello gmx-users, I want to calculate the average helicity of a peptide in last 20 ns of the simulation. g_helix is giving % helicity per residue during the specified period of time. Is there a way to do what I wish to calculate. Kindly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Helicity
Thanks. I am aware of all those commands. My question is specific to gromacs out, the file helicity.xvg has an output of the form: 9 @title Helicity per Residue 10 @xaxis label Residue 11 @yaxis label % of time 12 @TYPE xy 13 1 0 14 2 92.6148 15 3 86.8263 16 4 96.008 ..so on It is telling me residue 2 is 92 % of time (that I specified) helical. I want the average helicity of the peptide during the specified time. Thanks, sxn On Fri, Feb 6, 2015 at 3:11 PM, Diogo Vila Viçosa diogo.vic...@fc.ul.pt wrote: I Shivangi, There are several ways to calculate the average helicity. If you are using linux you can easily do that with a simple awk / bash script. In windows you can paste the number of residues in helical structure over time in an excel spreadsheet and calculate the average, etc.. I suppose you are using linux and my advice to you is: try to learn something about awk, sed, bash, etc... before you dive in into more complex things such as a MD simulation. Best regards, Diogo Vila Viçosa shivangi nangia shivangi.nan...@gmail.com escreveu no dia Fri Feb 06 2015 at 20:00:41: Hello gmx-users, I want to calculate the average helicity of a peptide in last 20 ns of the simulation. g_helix is giving % helicity per residue during the specified period of time. Is there a way to do what I wish to calculate. Kindly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Unable to install gromacs
Dear Gromacs Users We have been trying to install gromacs-5.0.4 on ubuntu 14.04 work station. We have installed all the prerequisites for the gromacs and whenever exicuting the cmake .. we got following error. - The C compiler identification is unknown -- The CXX compiler identification is unknown CMake Error at CMakeLists.txt:45 (project): The CMAKE_C_COMPILER: /usr/share/openmpi/mpicc is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CC or the CMake cache entry CMAKE_C_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. CMake Error at CMakeLists.txt:45 (project): The CMAKE_CXX_COMPILER: /usr/share/openmpi/mpicxx is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CXX or the CMake cache entry CMAKE_CXX_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. -- Configuring incomplete, errors occurred! See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeOutput.log. See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles /CMakeError.log. We didn't get what the error meaning. Kindly help us to overcome from the above mentioned error. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] no residue type with Amber99SB-ILDN ff
Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
Hi, What was the last thing written to the log files? Mark On Tue, Feb 3, 2015 at 2:01 PM, Felipe Villanelo el.maest...@gmail.com wrote: Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Unable to install gromacs
Hi, Seems Rahul just asked this question. As Dan said to him, normally you don't need MPI for running mdrun on a workstation. If you do, get the standard OpenMPI ubuntu package. Then, you can just configure GROMACS with -DGMX_MPI=on and everything will be detected. BTW, there should never be executable code installed in /usr/share, so don't do that or expect that. Mark On Fri, Feb 6, 2015 at 11:03 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Gromacs Users We have been trying to install gromacs-5.0.4 on ubuntu 14.04 work station. We have installed all the prerequisites for the gromacs and whenever exicuting the cmake .. we got following error. - The C compiler identification is unknown -- The CXX compiler identification is unknown CMake Error at CMakeLists.txt:45 (project): The CMAKE_C_COMPILER: /usr/share/openmpi/mpicc is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CC or the CMake cache entry CMAKE_C_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. CMake Error at CMakeLists.txt:45 (project): The CMAKE_CXX_COMPILER: /usr/share/openmpi/mpicxx is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CXX or the CMake cache entry CMAKE_CXX_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. -- Configuring incomplete, errors occurred! See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeOutput.log. See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles /CMakeError.log. We didn't get what the error meaning. Kindly help us to overcome from the above mentioned error. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Distance restraint between two chains' com
Dear Justin: Sorry to bother you again When I did a long flat-bottom distance restraint(about 2nm), I got the error message: “There is no domain decomposition for 8 nodes” So is there any way to do a long distance restraint properly. Best regards Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn* On Thu, Feb 5, 2015 at 7:51 PM, WT Ren rener...@gmail.com wrote: Dear Justin: Many thanks for your reply. I would like to test the new feature, but I have no much spare time recently. So it seems that I have to choose some atoms from the two chains seperately, and do distance restraint on these atoms. Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn* On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/5/15 2:39 AM, WT Ren wrote: Dear Gromacs Users, I am trying to apply a distance restraint between two chains' center of mass to prevent them diffusing far away from each other. As I known, the pull code seems only can restrain the distance to a reference distance with harmonic potential, while the distance restraint seems can not be applied to center of mass. So can anyone help on this issue? I am assuming that you want to apply some sort of flat-bottom potential, to be applied only when the chains move a certain distance. Indeed the pull code cannot do that at present, but a flat-bottom potential is in development if you want to test it: https://gerrit.gromacs.org/#/c/3947/ -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Covalent bond/crosslink formation with calcium
Thank you for the swift reply! We have decided against defining covalent bonds and went with the calcium-within-peptide-fiber configuration, but we have run into another problem, in that some of the calcium cations vanish from the unit cell that the fiber is in, and appear in the next unit cell, when we run an energy minimization. The missing cations are all on the same side of the peptide fiber and form a neat half-cylinder on the adjecent unit cell, so we are fairly certain that the problem has to do with our box definition. However, the entire structure is within our dodecahedral box prior to energy optimization. Is there any reason that the calciums would change position after energy minimization? Do we have to redefine our box afterwards? Thanks in advance, -Turgay 2015-02-02 15:01 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 2/2/15 7:08 AM, Turgay Cakmak wrote: Dear Gromacs users, We are simulating a large nanofiber assembly composed of repeating units of peptides, and we have been trying to see how the addition of calcium would affect its behavior. We have already tried adding calcium ions in a random distribution, which we successfully did. But we also would like to insert calcium ions directly within the fiber structure, near areas with negative charges that the calcium cation can potentially bind. Is such a configuration possible (or sensible) to simulate in Gromacs? Anything is possible. You'll have to justify if it's sensible :) Likewise, we would like to specify a number of covalent bonds between some of these side chains and the calcium ions, representing a well-crosslinked system. Is this possible, and if so, do you know of a suitable set of calcium forcefield parameters for the task? I have never heard of such bonded parameters. People usually just modify nonbonded parameters to get proper coordination geometry. Divalent metal ions are quite tricky, and most force field parameters are pretty bad approximations of the true nature of the actual interactions. You'll almost certainly have to derive suitable parameters, which will involve reparametrization of charges, because charge-transfer effects would be significant in such a complex. Simply slapping a covalent bond between some peptide group and an ion with +2 charge is likely too crude to be realistic. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
On 2/6/15 8:10 AM, Ahmet yıldırım wrote: There isnt any breaks in chains. I checked it. But i use the middle domain of a structure. It means i deleted N-terminal and C-terminal domains. But it shouldnt be a problem? Without seeing your full screen output and providing the PDB file for download somewhere, there's no point in guessing. pdb2gmx finds a zwitterionic, standalone lysine. Clearly there is a problem, otherwise pdb2gmx wouldn't tell you there is one :) -Justin 2015-02-06 14:04 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 8:03 AM, Ahmet yıldırım wrote: LYS is NOT termini residue. pdb2gmx thinks it is. Check your input coordinate file (and screen output, which tells you where any breaks in chains occur). -Justin 2015-02-06 14:01 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
On 2/6/15 8:03 AM, Ahmet yıldırım wrote: LYS is NOT termini residue. pdb2gmx thinks it is. Check your input coordinate file (and screen output, which tells you where any breaks in chains occur). -Justin 2015-02-06 14:01 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraints and free energy calculations
On 2/5/15 6:59 AM, Kortzak, Daniel wrote: Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly: 1. Start with ion in binding site 2. Turn on position restraints (since this only one atom I don't have to care about orientation etc.) 3. Decouple (And do the same for a ion in bulk solution in another simulation.) First of all is this sensible or are there better ways of doing this? Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Can I do 2. by normal position restraints in my topology or do I have to use a pull code? The former would be more easy to execute but the manual entry for the restraint-lambdas sounds like I have to do the latter. A more precise version of my question would be: Has the decoupling/annihilating procedure (in particular the value of the restraint-lambda) any effect on the position restraints defined in the [moleculetype] section of the decoupled molecule? Then another thing is, that it would be more convenient (convenient for me because I need less jobs in the queue I am not claiming that this would be more efficient) to do both decoupling of an ion in the protein and coupling another ion in solution in the same simulation. But as far as I understand the couple-moltype approach, I can only decouple an ion in protein and decouple another ion in solution which would give useless results if do this in the same simulation. The only solution to this I see, is to introduce dummy atoms and use the A-B-topology approach. Is this correct? Best regards and thanks in advance for reading, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
LYS is NOT termini residue. 2015-02-06 14:01 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
There isnt any breaks in chains. I checked it. But i use the middle domain of a structure. It means i deleted N-terminal and C-terminal domains. But it shouldnt be a problem? 2015-02-06 14:04 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 8:03 AM, Ahmet yıldırım wrote: LYS is NOT termini residue. pdb2gmx thinks it is. Check your input coordinate file (and screen output, which tells you where any breaks in chains occur). -Justin 2015-02-06 14:01 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraints and free energy calculations
Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Hi Justin, thanks for your fast reply. So far I did not consider this because on alchemistry.org they say beginners should start with the decoupling approach and all the papers I read so far also do only the decoupling approach (even in the simple case of a single ion binding to a protein). But of course this is no reason why I should not try the pulling. One real problem might be that the binding site is buried relatively deep in the protein. First I have to read a little more but soon I will be back with questions regarding the pulling method :) Nevertheless I am still wondering about the other questions I asked (just curiosity, maybe I at some point this will be important for me). Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no residue type with Amber99SB-ILDN ff
I realized my mistake :) Sorry. There was a few missing atoms and residues in the .pdb file. I had completed them using pymol and amber xleap tool. I hadnt used chain identifier while i added these missing atoms to the .pdb file. But the other all residues had a chain identifier in the .pdb file. So pdb2gmx's head was confused. But it works now. And as you said before http://comments.gmane.org/gmane.science.biology.gromacs.user/62384 pdb2gmx dont need to the N and C prefixes in the 4.6.x series. I tested it. 2015-02-06 14:11 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 8:10 AM, Ahmet yıldırım wrote: There isnt any breaks in chains. I checked it. But i use the middle domain of a structure. It means i deleted N-terminal and C-terminal domains. But it shouldnt be a problem? Without seeing your full screen output and providing the PDB file for download somewhere, there's no point in guessing. pdb2gmx finds a zwitterionic, standalone lysine. Clearly there is a problem, otherwise pdb2gmx wouldn't tell you there is one :) -Justin 2015-02-06 14:04 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 8:03 AM, Ahmet yıldırım wrote: LYS is NOT termini residue. pdb2gmx thinks it is. Check your input coordinate file (and screen output, which tells you where any breaks in chains occur). -Justin 2015-02-06 14:01 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/6/15 7:58 AM, Ahmet yıldırım wrote: 4 letter residue names of termini in pdb file are in the columns 18-22. I think they are correct columns? The problem, from the error message, is that you have a standalone LYS (a zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force fields (as implemented) can't handle such a species due to modifications of backbone charges when applying N- and C-terminal modifications. To use this force field with this system, you need to introduce a new residue that defines the zwitterion correctly. -Justin 2015-02-06 13:15 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with the AMBER99SB-ILDN ff. My command: pdb2gmx -f protein.pdb -o protein.gro -p protein.top Fatal error: In the chosen force field there is no residue type for 'LYS' as a standalone (starting ending) residue The pdb2gmx gives this error though terminal residues are prefixed with N and C. Maybe those prefixes are in the wrong columns of your input .pdb file. Could there be something wrong with the input .pdb file? But i dont get this error with another forcefield, 43a2. GROMOS force fields handle termini differently from AMBER, so that's expected. Mark -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/
