[gmx-users] pdb2gmx: intra-chain disulfide bond missing problem
Dear GROMACS users, Can I ask a disulfide bond question if possible? The link below is my protein L50K.pdb with 5 disulfide bonds. https://copy.com/kPLlSianI4LtohNy After using gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge interactive one of the disulfide bonds (i.e. Heavy Chain, HC 236-310) does not show up in the interactive prompt. As a result, they become -SH instead of -S-S- in the output .gro file (also in the link). I tried to search solutions but could not find the answer for this intra-chain disulfide bond missing problem. Could you please help me? Thank you very much. Yours sincerely Cheng (I was trying to upload the PDB file by attachment. But it seems that the mail has not been approved. So I use a link instead.) -- 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: Can I change the margin 10% to a higher value in the specbond.dat ?
Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the reference length in specbond.dat cannot cover all of the 5 Cys SG distance. I understand that a typical disulfide bond should be about 2.05 Å in length. However, if I still want to keep them, can I change the 10% margin to a higher value (e.g. 15%)? Thank you very much. Yours sincerely Cheng (Thank you for Justin's reply at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html Would it be possible if I can simply reply to you for the thread instead of creating a new one?) -- 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] Syntax to use gmx convert-tpr
Dear GROMACS experts, Can I ask if the following commandlines are correct for extending simulations? gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append (My job.sh can be found at https://copy.com/lrFubrlq9fos04Zy) My questions are: 1) For the 1st job, there are no .trr and .edr files. So the convert-tpr will be ignored? 2) Should I use -f md_0_1.trr or -f md_0_1.cpt as shown on http://manual.gromacs.org/programs/gmxconverttpr.html ? 3) What is index.ndx file used for? I cannot find them as outputs of a simulation. Do I need to include that? Thank you very much. Yours sincerely Cheng -- 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] Floating point exception for g_rms
Dear GROMACS experts, (Relevant files can be found on https://copy.com/7DMkn6OxJBqEZtqh) I have been told in the error file: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000 -- mpirun noticed that process rank 0 with PID 3 on node node-080 exited on signal 8 (Floating point exception). -- when I tried to submit a job with commandline below on our cluster: echo 2 2 | gerun g_rms -s md_0_1.tpr -f md_0_1.xtc Can I ask what is incorrect in my job? Thank you very much. Yours sincerely Cheng -- 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] how to assign options of the same type?
Dear GROMACS, Can I ask how to assign options of the same type? For example, on the website of http://manual.gromacs.org/current/programs/gmx-mdrun.html It is said in the Synopsis: [-o [.trr/.cpt/...] I want to name the output files as md.trr and md.cpt. However, the followings do not work: -o md.trr md.cpt -o md.trr/md.cpt -o md.trr -o md.cpt So do you know what is the syntax? Thank you very much. Yours sincerely Cheng -- 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] Can I ask how to extend my simulations?
Dear GROMACS, Can I ask how to extend my simulations? I would like to run a 50 ns job. Because of the cluster limitation, I need to use several jobs to complete that. ## Step1: grompp After using grompp on my PC, I got the input file md_0_1.tpr: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr ## Step2: mdrun As I see on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://manual.gromacs.org/current/programs/gmx-mdrun.html Can I ask if the following is correct in a job.sh file? (Initially, md_0_1.tpr and job.sh are the only files in the folder.) (I am still not sure how -cpi, -append, -maxh should be properly used. Do I also need to submit a second job with waiting dependency on the first job, what is the difference in the .sh file?) (In the following, if 24 hours is assigned to each job, can I still get the .xtc file after the first job has finished?) #!/bin/bash -l #$ -S /bin/bash #$ -l h_rt=24:00:0 #$ -l mem=4G #$ -l tmpfs=15G #$ -N MD #$ -pe openmpi 24 #$ -cwd module unload compilers module unload mpi module unload mkl module load compilers/intel/13.0/028_cxx11 module load mpi/openmpi/1.6.5/intel.13.0-028_cxx11 module load atlas/3.10.1/intel.13.0-028_cxx11 module load fftw/3.3.4/double/intel.13.0-028_cxx11 module load gromacs/5.0/openmpi/intel.13.0-028_cxx11 gerun mdrun_mpi -deffnm md_0_1 -cpi -maxh 23 ## Thank you very much. Yours sincerely Cheng -- 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] Can we convert one job into many serial jobs?
Dear GROMACS, I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our cluster. When the nodes required are too many (e.g. more than 8), jobs always take a long time to wait in the queue. So I wonder if there is a possibility that we can 1) convert the job into many serial jobs? 2) convert the job into several openmpi jobs but with only 1 node in each job? When serial jobs are submitted, hundreds of jobs can be run within just a few minutes. Thank you very much. Yours sincerely Cheng -- 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: can we use a file to specify the protonation instead of using -inter?
Dear GROMACS experts, Can I ask is there a more efficient way to deal with the -inter option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again. Would it be possible if the command line can link to a file, which specifies the protonation for individual residues? Thank you very much. Yours sincerely Cheng -- 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] echo 15 y 1 1 ...... failed for gmx pdb2gmx with -merge
Dear GROMACS researchers, I was trying to assign the protonation status in one go by the following: echo 15 y 1 1 1 .. | gmx pdb2gmx -f HC_A227E.pdb -o HC_A227E_processed.gro -water spce -inter -ignh -merge interactive In the commandline above, the .. means the protonation status for different chargeable residues. Because I have an inter-chain disulfide bond in my two-chain protein, I have to use -merge to keep this inter-chain disulfide bond. The second interactive prompt is to ask if I want to merge these two chains. So my answer is y. However, it seems that the echo command could not be recognised if y is used and I got the following error message: Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain starting with residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping termini)? [n/y] --- Program gmx, VERSION 5.0.4 Source code file: /home/lanselibai/Cheng/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 1571 Fatal error: Error reading from stdin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- So can I ask how to use echo to merge chains so that I can assign protonation status in one go? Thank you very much. Yours sincerely Cheng -- 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] gromacs installing problems with "cmake .."
Dear Gromacs users, I got a list of errors after running "cmake ..". I am sure the "cmake" itself is already installed. I am installing Gromacs 5.1.4 on ubuntu-14.04.1 on VMwarePlayer on a Dell PC. Can I ask how to solve this? Thank you. Yours sincerely Cheng ucbepan@ubuntu:/mnt/hgfs/Documents/gromacs-5.1.4/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- The CXX compiler identification is unknown CMake Error: your CXX compiler: "CMAKE_CXX_COMPILER-NOTFOUND" was not found. Please set CMAKE_CXX_COMPILER to a valid compiler path or name. -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Warning at cmake/gmxTestCompilerProblems.cmake:41 (message): The ids of the C and C++ compilers do not match (GNU and , respectively). Mixing different C/C++ compilers can cause problems. Call Stack (most recent call first): CMakeLists.txt:310 (gmx_test_compiler_problems) CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message): The versions of the C and C++ compilers do not match (4.8.2 and , respectively). Mixing different C/C++ compilers can cause problems. Call Stack (most recent call first): CMakeLists.txt:310 (gmx_test_compiler_problems) CMake Error at cmake/gmxManageSimd.cmake:67 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): cmake/gmxManageSimd.cmake:261 (gmx_give_fatal_error_when_simd_support_not_found) CMakeLists.txt:648 (gmx_manage_simd) -- Configuring incomplete, errors occurred! See also "/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log". See also "/mnt/hgfs/Documents/gromacs-5.1.4/build/CMakeFiles/CMakeError.log". -- 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] How to extend my incompleted simulation? (not extend a completed one)
Hi Alex, Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, I still ONLY got the four files WITHOUT cpt file. ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log I know the link http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, but is it for extending a completed job? In my case, I want to continue a incompleted job. Thank you. Yours sincerely Cheng ____ From: Zhang, Cheng Sent: 29 December 2016 18:23 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Zhang, Cheng Subject: How to extend my incompleted simulation? (not extend a completed one) Dear Gromacs, I would like to extend my simulation. 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr". Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr". Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but WITHOUT a cpt file (why?): ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log So I want to continue the simulation from the end of 5 ns. How should I do this? I am not quite sure if I understand correctly from http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also feel this link does not address my problem, as the tpr file was not changed in my case. Thank you. Yours sincerely Cheng -- 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] How to extend my incompleted simulation? (not extend a completed one)
Dear Gromacs, I would like to extend my simulation. 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr". Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr". Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but WITHOUT a cpt file (why?): ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log So I want to continue the simulation from the end of 5 ns. How should I do this? I am not quite sure if I understand correctly from http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also feel this link does not address my problem, as the tpr file was not changed in my case. Thank you. Yours sincerely Cheng -- 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] How to extend my incompleted simulation? (not extend a completed one)
Hi Justin, Thank you very much. It worked as you said [] Yes, I was only using 10 min in the beginning, so no cpt file could be generated. Yours sincerely Cheng From: Zhang, Cheng Sent: 29 December 2016 19:02:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: How to extend my incompleted simulation? (not extend a completed one) Hi Alex, Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, I still ONLY got the four files WITHOUT cpt file. ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log I know the link http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, but is it for extending a completed job? In my case, I want to continue a incompleted job. Thank you. Yours sincerely Cheng ____ From: Zhang, Cheng Sent: 29 December 2016 18:23 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Zhang, Cheng Subject: How to extend my incompleted simulation? (not extend a completed one) Dear Gromacs, I would like to extend my simulation. 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr". Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr". Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but WITHOUT a cpt file (why?): ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log So I want to continue the simulation from the end of 5 ns. How should I do this? I am not quite sure if I understand correctly from http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also feel this link does not address my problem, as the tpr file was not changed in my case. Thank you. Yours sincerely Cheng -- 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] Reading tpx file (md_0_1.tpr) version 110 with version 100 program
Dear Gromacs, I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr" to generate the tpr file on my own PC. Then I submitted it to our university computer cluster, in which an older version is installed, and I got the Fatal error: Reading tpx file (md_0_1.tpr) version 110 with version 100 program I know I should use the same old version to generate the tpr file. But should I unstall the newer one, and install the older one? Can I use the newer Gromacs to generate the old tpr file? Thank you. Yours sincerely Cheng -- 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] How to put excipients into the simulation box?
Dear Gromacs Researchers, Can I ask how to put excipients (e.g. sucrose, trehalose) into the simulation box together with protein, salt and water? Those excipients do not strongly interact with proteins, so they could not be treated as protein-ligand complex. I learned how to prepare the protein-salt-water system by Justin's tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I wonder if excipients can also be added similarly as Na+ and Cl-? Thank you. Yours sincerely Cheng -- 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] How to extend simulation?
Thank you. So if the below is correct, and it will run for 100 ns? convert-tpr -s previous.tpr -extend 10 -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt -- Original -- From: "Justin Lemkul";<jalem...@vt.edu>; Date: Tue, Apr 4, 2017 02:12 AM To: "gmx-users"<gmx-us...@gromacs.org>; Subject: Re: [gmx-users] How to extend simulation? On 4/3/17 2:07 PM, ZHANG Cheng wrote: > (Following Justin's suggestion) > > > Dear Gromacs Researchers, > My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to > extend it to 100 ns. > > > As shown on > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > > Should I use the following two lines of code for the files in the same folder? > If the "deffnm" is set correctly? > But in this case, will the new simulation still only have 10 ns? > No. > > convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr If you replace "timetoextendby" with some sensible value of time (ps), then this means "next.tpr" will specify some longer amount of time to run. > gmx mdrun -deffnm next -cpi previous.cpt ...which is then passed to mdrun here. This says "run the longer simulation specified in next.tpr, but start from the point specified in previous.cpt rather than starting over from time zero." -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] How to extend simulation?
(Following Justin's suggestion) Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? If the "deffnm" is set correctly? But in this case, will the new simulation still only have 10 ns? convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt Thank you. Yours sincerely Cheng -- 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] How to extend simulation by changing the mdp file?
Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt gmx mdrun -deffnm new -cpi -append Thank you. Yours sincerely Cheng -- 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] Magic Number Error in XTC file (read 0, should be 1995)
Dear Gromacs, I am trying to analyse my xtc file (40 ns) using: echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact However, it shows: ... Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ... Then I re-run the MD from the start from a same tpr file for 0.39 ns and run the "trjconv", and it works all fine. So I think, maybe the 40 ns xtc file has something wrong during the MD. But the 40 ns MD could still be continued from a cpt file, so I am not sure where it actually goes wrong. Thank you. Yours sincerely Cheng The whole log for "trjconv" of the 40 ns MD: :-) GROMACS - gmx trjconv, VERSION 5.1.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, VERSION 5.1.1 Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 Command line: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact Will write xtc: Compressed trajectory (portable xdr format): xtc Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Group 0 ( System) has 127073 elements Group 1 (Protein) has 8850 elements Group 2 ( Protein-H) has 4351 elements Group 3 (C-alpha) has 645 elements Group 4 ( Backbone) has 1935 elements Group 5 ( MainChain) has 2785 elements Group 6 ( MainChain+Cb) has 3194 elements Group 7 (MainChain+H) has 3816 elements Group 8 ( SideChain) has 5034 elements Group 9 (SideChain-H) has 1566 elements Group10 (Prot-Masses) has 8850 elements Group11 (non-Protein) has 118223 elements Group12 ( Water) has 117684 elements Group13 (SOL) has 117684 elements Group14 ( non-Water) has 9389 elements Group15 (Ion) has 539 elements Group16 ( NA) has 155 elements Group17 ( CL) has 384 elements Group18 ( Water_and_ions) has 118223 elements Select a group: Reading frame 0 time0.000 Precision of md_0_1.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 0 time0.000 Reading frame 1 time 10.000-> frame 1 time 10.000 Reading frame 2 time 20.000-> frame 2 time 20.000 Reading frame 3 time 30.000-> frame 3 time 30.000 Reading frame 4 time 40.000-> frame 4 time 40.000 Reading frame 5 time 50.000-> frame 5 time 50.000 Reading frame 6 time 60.000-> frame 6 time 60.000 Reading frame 7 time 70.000-> frame 7 time 70.000 Reading frame 8 time 80.000-> frame 8 time 80.000 Reading frame 9 time 90.000-> frame 9 time 90.000 Reading frame 10 time 100.000-> frame 10 time 100.000 Reading frame 11 time 110.000 Reading frame 12 time 120.000 --- Program gmx trjconv, VERSION 5.1.1 Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/fileio/xtcio.c, line: 90 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)
Hi Justin, Thank you. But how can I know where it goes wrong, and how can I avoid that? If the trajectory is corrupt, why this 40 ns MD can still be continued to longer MD? Why it is okay in the beginning, but becomes corrupt later? My MD is a protein with 203 glycines in a 10x10x10 ns box filled with water and NaCl. -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:09 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Magic Number Error in XTC file (read 0, should be 1995) I also run "gmx check" to examine what is wrong: gmx check -s1 md_0_1.tpr -f md_0_1.xtc However, the same thing happened: Command line: gmx check -s1 md_0_1.tpr -f md_0_1.xtc Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Reading frame 0 time0.000 # Atoms 127073 Precision 0.001 (nm) Reading frame 1 time 10.000 Reading frame 2 time 20.000 Reading frame 3 time 30.000 Reading frame 4 time 40.000 Reading frame 5 time 50.000 Reading frame 6 time 60.000 Reading frame 7 time 70.000 Reading frame 8 time 80.000 Reading frame 9 time 90.000 Reading frame 10 time 100.000 Reading frame 11 time 110.000 Reading frame 12 time 120.000 --- Program gmx check, VERSION 5.1.1 Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/fileio/xtcio.c, line: 90 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Sun, Aug 13, 2017 10:52 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Magic Number Error in XTC file (read 0, should be 1995) Dear Gromacs, I am trying to analyse my xtc file (40 ns) using: echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact However, it shows: ... Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ... Then I re-run the MD from the start from a same tpr file for 0.39 ns and run the "trjconv", and it works all fine. So I think, maybe the 40 ns xtc file has something wrong during the MD. But the 40 ns MD could still be continued from a cpt file, so I am not sure where it actually goes wrong. Thank you. Yours sincerely Cheng The whole log for "trjconv" of the 40 ns MD: :-) GROMACS - gmx trjconv, VERSION 5.1.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, VERSION 5.1.1 Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 Command line: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact Will write xtc: Compressed trajectory (portable xdr format): xtc Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Group 0 ( System) has 127073 elements Group 1 (Protein) has 8850 elements Group 2 ( Protein-H) has 4351 elements Group 3 (
Re: [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)
Hi Justin, Thank you for explaining that. You said "a more reliable system", what does this mean? It is my first time adding glycines to my protein using OPLS-AA/L force field. Do you think this might be the reason, and should I switch to another force field? My procedure is as follows: 1) I get the glycine and protein pdb, convert them to .gro files using gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce -inter 2) then I add the protein.gro into a box, get the protein_newbox.gro: gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic 3) then I add glycines to this box: gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o protein_203_glycine.gro 4) then I do the exactly the same thing according to your tutorial, i.e. solvent with water, add ions, energy minimization, NVT, NPT, and finally the MD. Can I ask if the procedure is correct? Would you please recommend some tutorial for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)? Thank you. -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:25 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re: Magic Number Error in XTC file (read 0, should be 1995) Hi Justin, Thank you. But how can I know where it goes wrong, and how can I avoid that? If the trajectory is corrupt, why this 40 ns MD can still be continued to longer MD? Why it is okay in the beginning, but becomes corrupt later? My MD is a protein with 203 glycines in a 10x10x10 ns box filled with water and NaCl. -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:09 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Magic Number Error in XTC file (read 0, should be 1995) I also run "gmx check" to examine what is wrong: gmx check -s1 md_0_1.tpr -f md_0_1.xtc However, the same thing happened: Command line: gmx check -s1 md_0_1.tpr -f md_0_1.xtc Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Reading frame 0 time0.000 # Atoms 127073 Precision 0.001 (nm) Reading frame 1 time 10.000 Reading frame 2 time 20.000 Reading frame 3 time 30.000 Reading frame 4 time 40.000 Reading frame 5 time 50.000 Reading frame 6 time 60.000 Reading frame 7 time 70.000 Reading frame 8 time 80.000 Reading frame 9 time 90.000 Reading frame 10 time 100.000 Reading frame 11 time 110.000 Reading frame 12 time 120.000 --- Program gmx check, VERSION 5.1.1 Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/fileio/xtcio.c, line: 90 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Sun, Aug 13, 2017 10:52 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Magic Number Error in XTC file (read 0, should be 1995) Dear Gromacs, I am trying to analyse my xtc file (40 ns) using: echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact However, it shows: ... Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ... Then I re-run the MD from the start from a same tpr file for 0.39 ns and run the "trjconv", and it works all fine. So I think, maybe the 40 ns xtc file has something wrong during the MD. But the 40 ns MD could still be continued from a cpt file, so I am not sure where it actually goes wrong. Thank you. Yours sincerely Cheng The whole log for "trjconv" of the 40 ns MD: :-) GROMACS - gmx trjconv, VERSION 5.1.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts
[gmx-users] How to use the index.ndx when running rms?
Dear Gromacs, After running echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got a index.ndx file. Then I run echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns But still only 18 options could be recognised. The index.ndx file is already in the same folder. So how to use the index.ndx when running rms? Thank you. Yours sincerely Cheng -- 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] How to use the index.ndx when running rms?
Dear All, After a few tests, I finally got it. Actually, the command line below does NOT generate a new set of group. echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx Instead, it outputs ALL the 18 groups, each group contains its relevant atom numbers. After reading http://biophysics.med.jhmi.edu/~yliu120/tutorials.html It says: "If the index file you provide only contains one index group. Then the Gromacs program will not ask you for a choice of index groups since you only provide one to it." So I opened my initial .gro file, check the necessary numbers belong to my protein. Based on this information, I deleted unnecessary groups and numbers in the index.ndx file. Then run the command with "-n" option: gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n index.ndx And I successfully got the .xvg file. -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 11:50 PM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use the index.ndx when running rms? Hi Justin, Thank you. I added "-n index.ndx" to my rms command, but still got "Cannot read from input" error: Command line: gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n index.ndx Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Reading file md_0_1.tpr, VERSION 5.1.1 (single precision) Select group for least squares fit Group 0 ( System) has 127073 elements Group 1 (Protein) has 8850 elements Group 2 ( Protein-H) has 4351 elements Group 3 (C-alpha) has 645 elements Group 4 ( Backbone) has 1935 elements Group 5 ( MainChain) has 2785 elements Group 6 ( MainChain+Cb) has 3194 elements Group 7 (MainChain+H) has 3816 elements Group 8 ( SideChain) has 5034 elements Group 9 (SideChain-H) has 1566 elements Group10 (Prot-Masses) has 8850 elements Group11 (non-Protein) has 118223 elements Group12 ( Water) has 117684 elements Group13 (SOL) has 117684 elements Group14 ( non-Water) has 9389 elements Group15 (Ion) has 539 elements Group16 ( NA) has 155 elements Group17 ( CL) has 384 elements Group18 ( Water_and_ions) has 118223 elements Select a group: Select a group: Select a group: --- Program gmx rms, VERSION 5.1.1 Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/topology/index.cpp, line: 917 Fatal error: Cannot read from input For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------- -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 11:09 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to use the index.ndx when running rms? Dear Gromacs, After running echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got a index.ndx file. Then I run echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns But still only 18 options could be recognised. The index.ndx file is already in the same folder. So how to use the index.ndx when running rms? Thank you. Yours sincerely Cheng -- 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] How to configure the gro/itp/top files after running "insert-molecules"?
Dear Gromacs, I am doing a MD for a protein with glycines. For glycine, I use ) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter and got ) gly.gro ) posre_gly.itp ) topol_gly.top For protein, I use ) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive ) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic and got ) protein_processed.gro ) posre_protein.itp ) topol_protein.top ) protein_newbox.gro Then, I add glycines to the protein box: ) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro and got ) protein_glycine.gro, in which the 10 glycines were appended to the protein residues, as if they belong to the same protein molecule (is this normal?) Can I ask, 1) How can I configure the itp and top files (i.e. posre_gly.itp, topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD setting-up? E.g. should I combine them into one itp and one top file, how to do that? 2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy minimization. Is this the correct procedure? Thank you. Yours sincerely Cheng -- 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] How to configure the gro/itp/top files after running "insert-molecules"?
Dear Yujie Liu, Can I clarify your suggestions? copy gly.gro into protein.gro and changed the number of atoms: ) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro", the "protein_glycine.gro" already contains both protein residues and glycine ones, with 10 glycines following the proteins residues, as if they belong to a same molecule as shown below, so I can assume it is already copied as you suggested? (.. protein residues from 1 to 442) 442ALAHB1 6611 2.350 3.446 6.215 442ALAHB2 6612 2.294 3.373 6.080 442ALAHB3 6613 2.225 3.341 6.225 442ALA C 6614 2.443 3.233 6.346 442ALA OT 6615 2.357 3.205 6.425 442ALA O 6616 2.556 3.249 6.383 442ALA HO 6617 2.561 3.236 6.483 443GLY N 6618 5.163 5.878 5.519 443GLY H1 6619 5.235 5.930 5.475 443GLY H2 6620 5.179 5.780 5.507 443GLY H3 6621 5.075 5.902 5.479 443GLY CA 6622 5.160 5.910 5.663 443GLYHA1 6623 5.250 5.886 5.701 443GLYHA2 6624 5.145 6.008 5.672 443GLY C 6625 5.052 5.834 5.736 443GLY OT 6626 5.046 5.831 5.857 443GLY O 6627 4.965 5.774 5.662 443GLY HO 6628 4.898 5.727 5.720 (.. glycine molecules from 443 to 452) 10.88213 10.88213 10.88213 (this is the dimension of the box) - Then using #include?? ?? lines to add gly.itp into protein.top in suitable position ) Do you mean in the protein.top file, change ; Include Position restraint file #ifdef POSRES #include "posre_protein.itp" #endif into ; Include Position restraint file #ifdef POSRES #include "posre_protein.itp" #include "posre_gly.itp" #endif ? - changed [molecules] options to add the name and number of gly molecule. Note the information of posre_gly.itp. ) Do you mean in the protein.top file, change [ molecules ] ; Compound#mols Protein_chain_L 1 into [ molecules ] ; Compound#mols Protein_chain_L 1 (the "Protein_chain_L" refers to the protein) Protein 10 (the "Protein" refers to the glycine) ? -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 7, 2017 07:34 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to configure the gro/itp/top files after running "insert-molecules"? Dear Gromacs, I am doing a MD for a protein with glycines. For glycine, I use ) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter and got ) gly.gro ) posre_gly.itp ) topol_gly.top For protein, I use ) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive ) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic and got ) protein_processed.gro ) posre_protein.itp ) topol_protein.top ) protein_newbox.gro Then, I add glycines to the protein box: ) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro and got ) protein_glycine.gro, in which the 10 glycines were appended to the protein residues, as if they belong to the same protein molecule (is this normal?) Can I ask, 1) How can I configure the itp and top files (i.e. posre_gly.itp, topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD setting-up? E.g. should I combine them into one itp and one top file, how to do that? 2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy minimization. Is this the correct procedure? Thank you. Yours sincerely Cheng -- 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] How to obtain a proper structure for glycine?
Hi Dawid, Thank you. However, I still got three hydrogens after running: gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce -noter gly_processed.gro: Glycine aRginine prOline Methionine Alanine Cystine Serine10 3936GLY N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLYHA1 6 -0.078 0.147 -0.062 3936GLYHA27 -0.083 0.121 0.099 3936GLY C8 0.056 0.002 0.001 3936GLY O19 0.047 -0.127 0.004 3936GLY O2 10 0.163 0.059 -0.0070.43801 0.27464 0.19713 -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 7, 2017 02:20 AM To: "Mark Abraham"<mark.j.abra...@gmail.com>; "gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: [gmx-users] How to obtain a proper structure for glycine? Hi Mark, Thank you. I have a glycine PDB: ATOM 1 N GLY 3936 -1.908 -0.113 -0.081 1.00 20.00 ATOM 2 CA GLY 3936 -0.753 0.774 0.097 1.00 20.00 ATOM 3 C GLY 3936 0.558 0.024 0.014 1.00 20.00 ATOM 4 O GLY 3936 0.474 -1.274 0.036 1.00 20.00 ATOM 5 OXT GLY 3936 1.629 0.589 -0.066 1.00 20.00 END Then, I use: gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce and got gly_processed.gro: Glycine aRginine prOline Methionine Alanine Cystine Serine 8 3936GLY N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLY C6 0.056 0.002 0.001 3936GLY O17 0.047 -0.127 0.004 3936GLY O28 0.163 0.059 -0.007 0.43801 0.20480 0.16112 Can I ask, why there are still 3 hydrogens attached to the nitrogen? Yours sincerely Cheng -- Original -- From: "Mark Abraham";<mark.j.abra...@gmail.com>; Date: Mon, Aug 7, 2017 01:48 AM To: "gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How to obtain a proper structure for glycine? Hi, Prodrg is not gromacs software, so there is probably a better place to ask this question. I'd also look at their docs to find out how to suggest a carboxylic acid. Mark On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699...@qq.com> wrote: Dear Gromacs, I would like to perform simulations for a protein with glycines. I think I should use "insert-molecules" as shown on http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html So I went to PRODRG2 Server to obtain the glycine structure by "text drawing": O " N-C-C-O But I got a suggested structure of NH3-CH2-COO, instead of NH2-CH2-COOH. Can I ask why is that? Thank you. Yours sincerely Cheng -- 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] How to obtain a proper structure for glycine?
Hi Mark, Thank you. I have a glycine PDB: ATOM 1 N GLY 3936 -1.908 -0.113 -0.081 1.00 20.00 ATOM 2 CA GLY 3936 -0.753 0.774 0.097 1.00 20.00 ATOM 3 C GLY 3936 0.558 0.024 0.014 1.00 20.00 ATOM 4 O GLY 3936 0.474 -1.274 0.036 1.00 20.00 ATOM 5 OXT GLY 3936 1.629 0.589 -0.066 1.00 20.00 END Then, I use: gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce and got gly_processed.gro: Glycine aRginine prOline Methionine Alanine Cystine Serine 8 3936GLY N1 -0.191 -0.011 -0.008 3936GLY H12 -0.275 0.042 -0.002 3936GLY H23 -0.186 -0.055 -0.098 3936GLY H34 -0.190 -0.081 0.063 3936GLY CA5 -0.075 0.077 0.010 3936GLY C6 0.056 0.002 0.001 3936GLY O17 0.047 -0.127 0.004 3936GLY O28 0.163 0.059 -0.007 0.43801 0.20480 0.16112 Can I ask, why there are still 3 hydrogens attached to the nitrogen? Yours sincerely Cheng -- Original -- From: "Mark Abraham";<mark.j.abra...@gmail.com>; Date: Mon, Aug 7, 2017 01:48 AM To: "gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How to obtain a proper structure for glycine? Hi, Prodrg is not gromacs software, so there is probably a better place to ask this question. I'd also look at their docs to find out how to suggest a carboxylic acid. Mark On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699...@qq.com> wrote: Dear Gromacs, I would like to perform simulations for a protein with glycines. I think I should use "insert-molecules" as shown on http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html So I went to PRODRG2 Server to obtain the glycine structure by "text drawing": O " N-C-C-O But I got a suggested structure of NH3-CH2-COO, instead of NH2-CH2-COOH. Can I ask why is that? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Justin, Mark and Frank, Thank you so much for explaining it. Now I think I understand it. I was confusing because I thought, I should install/compile the xorg-dev by using "cmake". But actually, what you meant is, use "cmake" to compile Gromacs after installing xorg-dev. I tried as Frank suggested for the cmake command line, including "-DGMX_X11=on", using my original Gromacs 5.0.4 files. But some problems occurred on the cmake. But I managed to use VMD to visualise my xtc file. So it is okay for me now. Thank you for all your help! Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 04:27 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark, Yes, Justin gave me a link for Gromacs-2016.3, but not the link for xorg-dev. Do you mean, I should uninstall my current Gromacs 5.0.4, then install the Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on my Ubuntu? Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How the pH is reflected in Gromacs?
Dear Gromacs,I am simulating pH 4 condition. I interactively assign the protonation of chargeable residues of a protein based on PDB2PQR results by setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/). I do not add citrate or acetate molecules to the simulation box. So if the pH 4 condition could still be reflected? Thank you. Yours sincerely Cheng -- 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] How to use "gmx view" on Ubuntu?
Dear Mark, Yes, Justin gave me a link for Gromacs-2016.3, but not the link for xorg-dev. Do you mean, I should uninstall my current Gromacs 5.0.4, then install the Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3 on my Ubuntu? Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 11:27 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: How to use "gmx view" on Ubuntu? Dear Mark Abraham, Thank you very much for your updating. Sorry, could you please tell me where can I download the cmake file, or which command line to use, in order to compiling & installing? I have tried the below and they both worked, but "gmx view ??" still not work, with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 04:22 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use "gmx view" on Ubuntu? Dear Gromacs and Mark Abraham, Sorry, I am not familiar with compiling issue. I installed xorg-dev by: sudo apt-get install xorg-dev Then, I type cmake .. -DGMX_X11=on But I was told: CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/... ..." does not appear to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to use "gmx view" on Ubuntu? Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely Cheng -- 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] How to get the correct reference frame to run the rmsf?
Dear Gromacs, I try to use this command to calculate RMSF: echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq bfac.pdb -res -b 2 -e 3 My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is mandatory to assign a reference frame, so I use "md_0_1.tpr", which gives the frame at time 0 ns. However, I think I should use a frame which is a time-averaged position within 20-30 ns. Can I ask how to get this frame? In addition, the command line outputs a PDB file. So what does this conformation represents, time 0, 20 or 30 ns? Thank you. Yours sincerely Cheng -- 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 do not work for unstable conformations
Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, predicted by Rosetta with different ddG. After running pdb2gmx, I found that the structures with lower ddG (more stable) all perform okay; while structures with higher ddG (less stable) got fatal error: Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For example, I got fatal error for: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive But it works fine for: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just change to another stable mutant, but the first residue ASP is the same) But I could not figure out the exact reasons for the fatal error. I have attached two stable PDB and two unstable PDB: https://1drv.ms/f/s!AjIs-W_id1LzobIlN0o5fxW49-Fmmg Could you please help me to find out the reasons? Thank you very much. Yours sincerely Cheng All the screen output is below, quite long: -- lanselibai@ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$ gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive GROMACS:gmx pdb2gmx, VERSION 5.0.4 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive Select the Force Field: >From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15 Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading HC_V215W.pdb... Read 3342 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain starting with residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping termini)? [n/y] y Merged chains into joint molecule definitions at 1 places. There are 1 chains and 0 blocks of water and 442 residues with 3342 atoms chain #res #atoms 1 'L' 442 3342 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 815 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 54 Sorting it all out... Opening force field file
Re: [gmx-users] pdb2gmx do not work for unstable conformations
Dear Mark Abraham, Thank you so much for debugging it for me. The strange word could only be seen under Unix environment. After using dos2unix, the problem finally solves! I totally forgot to always use dos2unix. Thanks a lot for reminding me again! Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Sat, May 20, 2017 09:32 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: pdb2gmx do not work for unstable conformations Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, predicted by Rosetta with different ddG. After running pdb2gmx, I found that the structures with lower ddG (more stable) all perform okay; while structures with higher ddG (less stable) got fatal error: Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For example, I got fatal error for: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive But it works fine for: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just change to another stable mutant, but the first residue ASP is the same) But I could not figure out the exact reasons for the fatal error. I have attached two stable PDB and two unstable PDB: https://1drv.ms/f/s!AjIs-W_id1LzobIlN0o5fxW49-Fmmg Could you please help me to find out the reasons? Thank you very much. Yours sincerely Cheng All the screen output is below, quite long: -- lanselibai@ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$ gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive GROMACS:gmx pdb2gmx, VERSION 5.0.4 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive Select the Force Field: >From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15 Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading HC_V215W.pdb... Read 3342 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and
Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial
Dear Joao, Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that true that NVT needs to change two lines, while NPT and production run only need to change one line? Yours sincerely Cheng 1) In the NVT: ref_t = 370 370 ; reference temperature, one for each group, in K gen_temp = 370 ; temperature for Maxwell distribution 2) In the NPT: ref_t = 370 370; reference temperature, one for each group, in K 3) In the production run: ref_t = 370 370 ; reference temperature, one for each group, in K -- 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] mdp file for 370 K MD based on Justin's tutorial
Dear Gromacs, I am performing 370 K MD based on Justin's tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html After "Step Five: Energy Minimization", I need to do NVT, NPT and a production run. I think I need to change 300 K to 370 K in three mdp files. Specifically, 1) In the NVT: ref_t = 370 370 ; reference temperature, one for each group, in K gen_temp = 370 ; temperature for Maxwell distribution 2) In the NPT: ref_t = 370 370; reference temperature, one for each group, in K 3) In the production run: ref_t = 300 300 ; reference temperature, one for each group, in K Can I ask if these are the adjustments I need to do, and if there are something else I need? Thank you. Yours sincerely Cheng -- 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: Atom N used in the topology not found in the input (PDB) file
Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. However, the residue 1 in the PDB is: ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.581 14.101 -1.318 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.809 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.236 17.903 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.346 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.873 -3.080 1.00 0.00 H You can see that the first atom is just atom N, not missing. Can I ask why I still got this error? Another mutant file of the protein works totally fine for pdb2gmx. Its 1st residue ASP is the below, I could not see any big difference except slight difference in the coordinates. ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.586 14.106 -1.317 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.810 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.235 17.904 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.345 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.872 -3.080 1.00 0.00 H Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab). I will try the different water models. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 01:07 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Simulate protein at subzero condition in aqueous buffer Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] "cmake" failed to install
Dear Mark and Mario, Thank you very much. I delete the gromacs and redo the cmake and it works now. Yours sincerely Cheng -- Original -- From: "mario";<ma...@exactas.unlpam.edu.ar>; Date: Thu, Jun 1, 2017 04:07 PM To: "ZHANG Cheng"<272699...@qq.com>; Cc: "mario"<ma...@exactas.unlpam.edu.ar>; "gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: [gmx-users] "cmake" failed to install Seems to be an old problem. You should read this https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097312.html > After following Mario's link, I still could not solve it. The same problem > happens. > > > My command line is: > > > lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake .. > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > -- The CXX compiler identification is GNU 4.8.4 > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU > acceleration > -- Performing Test CXXFLAGS_PRAGMA > -- Performing Test CXXFLAGS_PRAGMA - Success > -- Performing Test CXXFLAGS_WARN > -- Performing Test CXXFLAGS_WARN - Success > -- Performing Test CXXFLAGS_WARN_EXTRA > -- Performing Test CXXFLAGS_WARN_EXTRA - Success > -- Performing Test CXXFLAGS_WARN_UNDEF > -- Performing Test CXXFLAGS_WARN_UNDEF - Success > -- Performing Test CXXFLAGS_WARN_REL > -- Performing Test CXXFLAGS_WARN_REL - Success > -- Performing Test CXXFLAGS_EXCESS_PREC > -- Performing Test CXXFLAGS_EXCESS_PREC - Success > -- Performing Test CXXFLAGS_COPT > -- Performing Test CXXFLAGS_COPT - Success > -- Performing Test CXXFLAGS_NOINLINE > -- Performing Test CXXFLAGS_NOINLINE - Success > CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message): > The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4, > respectively). Mixing different C/C++ compilers can cause problems. > Call Stack (most recent call first): > CMakeLists.txt:310 (gmx_test_compiler_problems) > > > > > CMake Error at cmake/gmxManageSimd.cmake:67 (message): > Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 > SIMD > (slower). > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:261 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:648 (gmx_manage_simd) > > > > > -- Configuring incomplete, errors occurred! > See also > "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log". > See also > "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log". > > > > > > -- Original -- > From: "mario";<ma...@exactas.unlpam.edu.ar>; > Date: Thu, Jun 1, 2017 02:44 PM > To: "gmx-users"<gmx-us...@gromacs.org>; > Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; > "ZHANG Cheng"<272699...@qq.com>; > Subject: Re: [gmx-users] "cmake" failed to install > > > > Dear Cheng: > I solved that problem by following step by step instructions of the next > page: > > https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/ > > Best Regards > Mario Campo > Dpto Física - UNLPam > La Pampa Argentina > >> Dear Gromacs, >> I did the below on Ubuntu 14.04: >> >> >> tar xfz gromacs-5.1.4.tar.gz >> cd gromacs-5.1.4 >> mkdir build >> cd build >> >> >> >> Then, I got error message when running: >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON >> >> >> The error log files can be found here: >> https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ >> >> >> Can I ask how to solve this? >> >> >> Thank you. >> >> >> Yours sincerely >> Cheng >> -- >> 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] "cmake" failed to install
Dear Gromacs, I did the below on Ubuntu 14.04: tar xfz gromacs-5.1.4.tar.gz cd gromacs-5.1.4 mkdir build cd build Then, I got error message when running: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON The error log files can be found here: https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ Can I ask how to solve this? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] "cmake" failed to install
After following Mario's link, I still could not solve it. The same problem happens. My command line is: lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- The CXX compiler identification is GNU 4.8.4 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_WARN_EXTRA -- Performing Test CXXFLAGS_WARN_EXTRA - Success -- Performing Test CXXFLAGS_WARN_UNDEF -- Performing Test CXXFLAGS_WARN_UNDEF - Success -- Performing Test CXXFLAGS_WARN_REL -- Performing Test CXXFLAGS_WARN_REL - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message): The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4, respectively). Mixing different C/C++ compilers can cause problems. Call Stack (most recent call first): CMakeLists.txt:310 (gmx_test_compiler_problems) CMake Error at cmake/gmxManageSimd.cmake:67 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): cmake/gmxManageSimd.cmake:261 (gmx_give_fatal_error_when_simd_support_not_found) CMakeLists.txt:648 (gmx_manage_simd) -- Configuring incomplete, errors occurred! See also "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log". See also "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log". -- Original -- From: "mario";<ma...@exactas.unlpam.edu.ar>; Date: Thu, Jun 1, 2017 02:44 PM To: "gmx-users"<gmx-us...@gromacs.org>; Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] "cmake" failed to install Dear Cheng: I solved that problem by following step by step instructions of the next page: https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/ Best Regards Mario Campo Dpto Física - UNLPam La Pampa Argentina > Dear Gromacs, > I did the below on Ubuntu 14.04: > > > tar xfz gromacs-5.1.4.tar.gz > cd gromacs-5.1.4 > mkdir build > cd build > > > > Then, I got error message when running: > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > > The error log files can be found here: > https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ > > > Can I ask how to solve this? > > > Thank you. > > > Yours sincerely > Cheng > -- > 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] pdb2gmx: Atom N used in the topology not found in the input (PDB) file
Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? Cheng ---Original--- From: "ZHANG Cheng"<272699...@qq.com> Date: 2017/5/19 22:37:52 To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "QQ"<272699...@qq.com>; Subject: pdb2gmx: Atom N used in the topology not found in the input (PDB) file Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. However, the residue 1 in the PDB is: ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.581 14.101 -1.318 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.809 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.236 17.903 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.346 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.873 -3.080 1.00 0.00 H You can see that the first atom is just atom N, not missing. Can I ask why I still got this error? Another mutant file of the protein works totally fine for pdb2gmx. Its 1st residue ASP is the below, I could not see any big difference except slight difference in the coordinates. ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.586 14.106 -1.317 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.810 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.235 17.904 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.345 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.872 -3.080 1.00 0.00 H Thank you. Yours sincerely Cheng -- 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: Atom N used in the topology not found in the input (PDB) file
Dear Justin, The command line that got fatal error is: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive The command line that works fine is: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just change to another mutant, but the first residue ASP is the same) I basically interactively assign the protonation state of each chargeable residues. All the screen output is below, quite long: -- lanselibai@ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$ gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive GROMACS:gmx pdb2gmx, VERSION 5.0.4 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive Select the Force Field: >From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15 Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading HC_V215W.pdb... Read 3342 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain starting with residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping termini)? [n/y] y Merged chains into joint molecule definitions at 1 places. There are 1 chains and 0 blocks of water and 442 residues with 3342 atoms chain #res #atoms 1 'L' 442 3342 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 815 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 54 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb Processing chain 1 'L' (3342 atoms, 442 residues) Which LYSINE type do you want for residue 24 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (LYSH) Type a number:1 Which LYSINE type do you want for residue 39 0. Not protonated (charge 0) (LYS) 1. Protonated (charge +1) (ARG) (here I just interactively assign protonation state) Identified residue ASP1 as a starting terminus. Identified residue CYS214 as a ending terminus. Identified residue
Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?
Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns 2) Is there a tutorial/manual for using python to extract coordinates at customised time and group? I will look at the "gmx traj -ox". Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Nov 24, 2017 00:20 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Does RMSD only consider the "relative" coordinate changes for the selected group? Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop. My understanding is: when doing the RMSD, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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] Does RMSD only consider the "relative" coordinate changes for the selected group?
Dear Justin and Peter, Thank you so much! I did not realise the meaning of two prompts until now. I was always using the same number for the two prompts. Thank you for the MDAnalysis! https://www.mdanalysis.org/pages/learning_MDAnalysis/ Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Nov 24, 2017 06:25 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Does RMSD only consider the "relative" coordinate changes for the selected group? Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns 2) Is there a tutorial/manual for using python to extract coordinates at customised time and group? I will look at the "gmx traj -ox". Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Nov 24, 2017 00:20 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Does RMSD only consider the "relative" coordinate changes for the selected group? Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop. My understanding is: when doing the RMSD, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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] Does RMSD only consider the "relative" coordinate changes for the selected group?
Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop. My understanding is: when doing the RMSD, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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] Why the index file does not contain the indices I want?
Dear Gromacs, After running echo r 66 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got the index.ndx file. However, all the sections are those default ones, without the 66th residue atoms I want: [ System ] [ Protein ] [ Protein-H ] .. [ Ion ] [ NA ] [ CL ] [ Water_and_ions ] May I ask how to obtain the indices for the residue 66? In addition, my protein has light chain (L) and heavy chain (H). So how to specify the 66th residue within the light chain by using "echo"? Thank you. Yours sincerely Cheng -- 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] How to run MD with longer recording interval to reduce the file size?
Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"? 3) Do you mean using "compressed-x-grps=Protein" will set xtc-grps as a group without waters and counterions? ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 08:34 PM To: "ZHANG Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to run MD with longer recording interval to reduce the file size? Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- 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] How to run MD with longer recording interval to reduce the file size?
Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- 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] How the index is recognised for values more than 99999?
Dear Gromacs,I am doing the RMSD calculation for a particular group of protein residues. My system also has water molecules so there are more than 9 atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so on. So if the index file for my group has an entry of 1, how can the gromacs know it is the 1st atom, instead of the 11th atom? Thank you. Yours sincerely Cheng -- 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] How the index is recognised for values more than 99999?
Hi Mark, I only calculate the RMSD for a particular group. So I need to use a index file, which explicitly indicates the atom indices within that group. 1) So if that group indices contain "1 2 3 ...", the Gromacs software will always assume they are 1st, 2nd, 3rd, ... atoms, instead of 11th, 12th, 13th, ... ? 2) And if I want the RMSD for the group containing atom 11th, 12th, 13th, ..., I need to write their indices as 11, 12, 13, ..., ? Thank you. Cheng -- Original -- From: "Mark Abraham";<mark.j.abra...@gmail.com>; Date: Wed, Dec 6, 2017 04:34 AM To: "gmx-users"<gmx-us...@gromacs.org>; Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How the index is recognised for values more than 9? Hi, The numbering of the coordinate file is not significant for this, precisely for that reason. Mark On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@qq.com> wrote: Dear Gromacs,I am doing the RMSD calculation for a particular group of protein residues. My system also has water molecules so there are more than 9 atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so on. So if the index file for my group has an entry of 1, how can the gromacs know it is the 1st atom, instead of the 11th atom? Thank you. Yours sincerely Cheng -- 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] What is the most reliable way to run repeats for reproducibility?
Hi Mark, Thank you very much. ) For the link you provide, I think I could not manipulate most of the computer resources, as I submit my jobs to our cluster, and the jobs are distributed to different available cores randomly. ) For "random seed" of velocity, I found here and I enabled this option: gen_vel = yes http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html So does it mean that it is better to use the same em.tpr and run different NVT,NPT,etc. for different repeats, so as to initialise it with different velocities? ) How the "natural chaotic divergence during equilibration" is reflected at which step? The link says: "The Central Limit Theorem tells us that in the case of infinitely long simulation all observables converge to their equilibrium values". But I think this "equilibrium" is not practical for protein in MD. For example, if I am running a protein at 370K, ultimately it will unfold, like boiling an egg in water, it takes 10 min. But in MD, the time scale is way more shorter, i.e. usually a few hundred ns scale. We could "never" see the proteins converges within that short period. So my understanding about "equilibrium" is the equilibration for temperature/pressure/density, but not the protein itself. Is that correct? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jan 10, 2018 09:11 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: What is the most reliable way to run repeats for reproducibility? Dear Gromacs, I can think of different ways of running repeats, after reading Justin's lysozyme tutorial. The 1st way: all starting from the same em.tpr after energy minimization (EM) and use em.tpr individually for subsequent steps (NVT, NPT and production MD): ) repeat 1: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 2: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 3: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD .. The 2nd way: all starting from the same md_0_1.tpr and use it for different production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? production MD ) repeat 2: same md_0_1.tpr?? production MD ) repeat 3: same md_0_1.tpr?? production MD .. The 3rd way: all starting from the same check point file within the production run and use it for the rest of the production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? same production MD for 50 ns ?? same .cpt file ?? production MD for another 200 ns ) repeat 2: same .cpt file ?? production MD for another 200 ns ) repeat 3: same .cpt file ?? production MD for another 200 ns .. Of course, the 3rd way is easier. But does it mean it may not cover enough conformations, as they tend to be more resembled from each other than the 1st approach? Is there a standard way to handle the repeats? Thank you. Yours sincerely Cheng -- 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] What is the most reliable way to run repeats for reproducibility?
Dear Gromacs, I can think of different ways of running repeats, after reading Justin's lysozyme tutorial. The 1st way: all starting from the same em.tpr after energy minimization (EM) and use em.tpr individually for subsequent steps (NVT, NPT and production MD): ) repeat 1: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 2: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 3: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD .. The 2nd way: all starting from the same md_0_1.tpr and use it for different production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? production MD ) repeat 2: same md_0_1.tpr?? production MD ) repeat 3: same md_0_1.tpr?? production MD .. The 3rd way: all starting from the same check point file within the production run and use it for the rest of the production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? same production MD for 50 ns ?? same .cpt file ?? production MD for another 200 ns ) repeat 2: same .cpt file ?? production MD for another 200 ns ) repeat 3: same .cpt file ?? production MD for another 200 ns .. Of course, the 3rd way is easier. But does it mean it may not cover enough conformations, as they tend to be more resembled from each other than the 1st approach? Is there a standard way to handle the repeats? Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns I got: 0.0002.767 0.1002.757 0.2002.736 ... ... Do you know what is the meaning of the second column? Thank you! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ... -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:02 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re:Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns I got: 0.0002.767 0.1002.757 0.2002.736 ... ... Do you know what is the meaning of the second column? Thank you! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may
[gmx-users] Which files does "-cpi -append" need?
Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Gradually, I have thousands of log files. So I used these commands to delete all of them in one go, : rm md_0_1.e* rm md_0_1.o* rm md_0_1.pe* rm md_0_1.po* I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete. However, after deleting all the log files, and then started a new run, I was told: Fatal error: File appending requested, but 1 of the 4 output files are not present or are named differently So it seems that the checkpoint information is also in one of those md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files? Thank you. -- 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] Which files does "-cpi -append" need?
Thank you very much Justin! Sorry I did not realise that. I will need to include an "except md_0_1.edr" in the deletion. But does it correct that I can delete all the log files? md_0_1.e md_0_1.o md_0_1.pe md_0_1.po -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Sat, Jan 20, 2018 00:45 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Which files does "-cpi -append" need? Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Gradually, I have thousands of log files. So I used these commands to delete all of them in one go, : rm md_0_1.e* rm md_0_1.o* rm md_0_1.pe* rm md_0_1.po* I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete. However, after deleting all the log files, and then started a new run, I was told: Fatal error: File appending requested, but 1 of the 4 output files are not present or are named differently So it seems that the checkpoint information is also in one of those md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files? Thank you. -- 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] Why gyration radius keep dropping?
Dear Gromacs, I am running MD at 500 K for my protein. I used this to analyse the gyration radius echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg I thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a dropping in the gyration radius, from ~2.6 nm to ~2.2 nm in 50 ns. Can I ask if this phenomenon is common? Cheng -- 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] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
I got it, Thank you very much for all the help! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:46 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re:Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ... ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:02 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re:Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns I got: 0.0002.767 0.1002.757 0.2002.736 ... ... Do you know what is the meaning of the second column? Thank you! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa&quo
[gmx-users] Alternative for do_dssp for secondary structure analysis?
Dear Gromacs, Can I ask if there is an alternative to do_dssp for secondary structure analysis? I am waiting for our IT staff to install the DSSP on our cluster. But there was some errors. https://github.com/UCL-RITS/rcps-buildscripts/issues/137 While still waiting for that, can I ask if Gromacs has other tools (e.g. STRIDE) for secondary structure analysis? Now I am using the VMD-Timeline tool, which uses the STRIDE http://webclu.bio.wzw.tum.de/stride/ Thank you. Yours sincerely Cheng -- 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] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?
Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign b-factor values to all the frames of one pdb file? Yours sincerely Cheng -- 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] Can I put b-factor into xtc file?
Thank you Mark for this fascinating tng format. I think I could not modify it using C/C++ at this moment. For your "easier approach", do you mean I can convert xtc to pdb frame with b-factor assigned, if I provide the b-factor file? How to do this? -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Feb 2, 2018 04:44 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I put b-factor into xtc file? Dear Gromacs, I have residue-based b-factor values for a protein. In the past, they were assigned to the b-factor columns of pdb files. It would take a lot of space if I extract all the pdb files. As the pdb files come from the xtc file, I wonder, if I can modify the xtc file directly? Thank you. Yours sincerely Cheng -- 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] Can I put b-factor into xtc file?
Dear Gromacs, I have residue-based b-factor values for a protein. In the past, they were assigned to the b-factor columns of pdb files. It would take a lot of space if I extract all the pdb files. As the pdb files come from the xtc file, I wonder, if I can modify the xtc file directly? Thank you. Yours sincerely Cheng -- 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] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?
Dear Gromacs, The scount.xvg file was obtained after running echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns The secondary structures listed are: 'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix' I ran the command for different proteins. It surprised me that the last '5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not have the '5-Helix', but why not just show them as 0? Can this be improved? Because I am using a script to read the scount.xvg files, so I want all the files have the same format. Thank you. Yours sincerely Cheng -- 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] Why "do_dssp" gives one more residue?
Dear Gromacs,
My protein only has 442 residues. After running
gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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Re: [gmx-users] Why "do_dssp" gives one more residue?
Dear Qinghua,
Yes, exactly! But the numbering is:
1-214: first chain
215-442: second chain
However, for the secondary structure codes:
214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",
215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",
442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",
443th:
"~"
Do you think the 443th line is the separator? So ignore the 443th line?
------ Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:20 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;"ZHANG
Cheng"<272699...@qq.com>;
Subject: Why "do_dssp" gives one more residue?
Dear Gromacs,
My protein only has 442 residues. After running
gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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Re: [gmx-users] Why "do_dssp" gives one more residue?
Dear Justin,
Thank you. But it does not make sense to me. Do you know if separator line is
always all the ~ ? If the separator line is following the 214th residue, the
215th residue should be the separator line, but why the 215th residue contains
the secondary structure?
You can find my files at
https://1drv.ms/f/s!AjIs-W_id1LzpOsT2Dktn9hIO7-eNA
If you use a text editor,
The 214th residue: line 248
The 215th residue: line 249
The pdb file (bfac.pdb) after the simulation is also in the link (without the
chain ID).
The original pdb I use contains two chains. After running "gmx pdb2gmx -f
protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge
interactive", the two chains are merged to keep the inter-chain disulfide bond,
and also the chain ID has been lost since then.
Thank you.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:34 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Why "do_dssp" gives one more residue?
Dear Qinghua,
Yes, exactly! But the numbering is:
1-214: first chain
215-442: second chain
However, for the secondary structure codes:
214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",
215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",
442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",
443th:
"~"
Do you think the 443th line is the separator? So ignore the 443th line?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:20 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;"ZHANG
Cheng"<272699...@qq.com>;
Subject: Why "do_dssp" gives one more residue?
Dear Gromacs,
My protein only has 442 residues. After running
gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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[gmx-users] How to search answers for previous posts?
Dear Gromacs, I know I can see all the post from https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ but can I search from this link? I do not want to download all of them to my PC. Thank you. Yours sincerely Cheng -- 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] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file
I would like to share my answer for chain separator issue for the "gmx do_dssp". Millions of thanks to Carsten! The "gmx do_dssp" will output an additional line as chain separator between two chains. We do NOT need to provide a "ss.map" file in our working directory, and the command will find the default "ss.map" file automatically, and the ss.xpm file will have a line of "" as the chain separator. I created my own ss.map file based on http://manual.gromacs.org/online/map.html, and got the "~~" as chain separator, which is the same as coils. So do not do this. -- 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] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file
Also, can the "map file format" page be updated with "chain separator"? http://manual.gromacs.org/online/map.html 9 ~ Coil 1 1 1 E B-Sheet 1 0 0 B B-Bridge 0 0 0 S Bend 0 0.5 0 T Turn 1 1 0 H A-Helix 0 0 1 I 5-Helix 0.5 0 0.5 G 3-Helix 0.5 0.5 0.5 = Chain_Separator 0.9 0.9 0.9 -- Original ------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Apr 6, 2018 10:13 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;"ZHANG Cheng"<272699...@qq.com>; Subject: chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file I would like to share my answer for chain separator issue for the "gmx do_dssp". Millions of thanks to Carsten! The "gmx do_dssp" will output an additional line as chain separator between two chains. We do NOT need to provide a "ss.map" file in our working directory, and the command will find the default "ss.map" file automatically, and the ss.xpm file will have a line of "" as the chain separator. I created my own ss.map file based on http://manual.gromacs.org/online/map.html, and got the "~~" as chain separator, which is the same as coils. So do not do this. -- 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] ss.xpm file: chain separator location? first residue showing first, or last residue showing first?
Dear Gromacs,
(Sorry I post this again as I have not got confirmed answer yet)
In the ss.xpm file for secondary structures, can I ask if the first residue
shows first, or last residue shows first? I could not find the description in
the file.
I also have a chain separator. Can I ask does it show in the beginning or
between the two chains?
(Sorry, I asked this question about chain separator before. But if the last
residue shows first, it is possible that the chain separator is between the two
chains. But I really want to confirm that. Or how can I get contact with the
author who wrote the "gmx do_dssp"?)
I found the original post for the source code at
http://repo.or.cz/gromacs.git/commit/5e4dd0a15de15237ec34ac287dca8e0aa01adb40
Can I ask how to use the "repo.or.cz" website? I am not sure how to register it.
I also emailed the author Carsten, but have not got reply.
Thank you.
Yours sincerely
Cheng
First a few lines:
---
/* XPM */
/* Created by: */
/*:-) GROMACS - gmx do_dssp, VERSION 5.1.1 (-: */
/* */
/* Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx */
/* Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 */
/* Command line: */
/* gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg
-tu ns */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "Secondary structure" */
/* legend: "" */
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"1064 443 8 1",
"~ c #FF " /* "Coil" */,
"E c #FF " /* "B-Sheet" */,
"B c #00 " /* "B-Bridge" */,
"S c #00 " /* "Bend" */,
"T c #00 " /* "Turn" */,
"H c #FF " /* "A-Helix" */,
"G c #FF00FF " /* "3-Helix" */,
"I c #FF9900 " /* "5-Helix" */,
--
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[gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?
Dear Gromacs, I use Command line: gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns and was told: Error in user input: Invalid command-line options Unknown command-line option -tu So why "gyrate" could not be supplied with "-tu ns" option? Thank you. Yours sincerely Cheng -- 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] ss.xpm file: first residue showing first, or last residue showing first?
Dear Gromacs,
In the ss.xpm file for secondary structures, can I ask if the first residue
shows first, or last residue shows first? Is this already written in the file?
I also have a chain separator. Can I ask does it show in the beginning or
between the two chains?
(Sorry, I asked this question about chain separator before. But if the last
residue shows first, it is possible that the chain separator is between the two
chains. But I really want to confirm that. Or how can I get contact with the
author who wrote the "gmx do_dssp"?)
Thank you.
Yours sincerely
Cheng
First a few lines:
---
/* XPM */
/* Created by: */
/*:-) GROMACS - gmx do_dssp, VERSION 5.1.1 (-: */
/* */
/* Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx */
/* Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 */
/* Command line: */
/* gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg
-tu ns */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "Secondary structure" */
/* legend: "" */
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"1064 443 8 1",
"~ c #FF " /* "Coil" */,
"E c #FF " /* "B-Sheet" */,
"B c #00 " /* "B-Bridge" */,
"S c #00 " /* "Bend" */,
"T c #00 " /* "Turn" */,
"H c #FF " /* "A-Helix" */,
"G c #FF00FF " /* "3-Helix" */,
"I c #FF9900 " /* "5-Helix" */,
--
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[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- 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] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
Hi Mark, Thank you for your help! Sorry I was totally confused. I thought I should delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand that. I should ) still keep the "define = -DPOSRES" in the mdp file ) still keep the "[ position_restraints ]" section in the itp file ) the only difference is, add "-r target.gro" where the "target.gro" can be the same as that for "-c" option. Thank you very much! Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Jan 16, 2019 09:51 PM To: "gromacs.org_gmx-users"; Subject: What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018? My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- 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] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?
Sorry for asking this. I now understand it. See post at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123809.html -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Jan 16, 2019 04:27 AM To: "gromacs.org_gmx-users"; Subject: Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro? In Gromacs 2018, -r is used to provide the restraint file for grompp. I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro: gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o MD.tpr So in the command above, should I use AllAtom.pdb or CG.pdb as the file for "-r"? I tried both, and both can work without errors. But which one is more logically correct? I think the CG.pdb should definitely work. But why AllAtom.pdb is still okay? -- 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] How the "Fmax" is determined without "emtol" in the mdp file?
I am doing an energy minimization in a vacuum condition. There is no "emtol" in the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown below. So how this "< 10" is determined? Steepest Descents converged to Fmax < 10 in 4063 steps Potential Energy = -2.3973977e+04 Maximum force = 9.8130465e+00 on atom 405 Norm of force = 1.5696382e+00 My mdp file is: integrator = steep nsteps = 1 nstxout = 0 nstfout = 0 nstlog = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = reaction-field rcoulomb = 1.1 epsilon_r= 15; 2.5 (with polarizable water) epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 -- 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] How the "Fmax" is determined without "emtol" in the mdp file?
Thank you so much, Justin and Mark! -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 18, 2019 09:55 PM To: "gromacs.org_gmx-users"; Subject: How the "Fmax" is determined without "emtol" in the mdp file? I am doing an energy minimization in a vacuum condition. There is no "emtol" in the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown below. So how this "< 10" is determined? Steepest Descents converged to Fmax < 10 in 4063 steps Potential Energy = -2.3973977e+04 Maximum force = 9.8130465e+00 on atom 405 Norm of force = 1.5696382e+00 My mdp file is: integrator = steep nsteps = 1 nstxout = 0 nstfout = 0 nstlog = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = reaction-field rcoulomb = 1.1 epsilon_r= 15; 2.5 (with polarizable water) epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 -- 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] How to visualise the dodecahedron in Pymol or VMD?
I use gmx editconf -f protein.pdb -d 5 -bt dodecahedron -o protein.gro to put the protein in a dodecahedron. However, when I open the protein.gro in pymol, and type "show cell", only a triclinic box is shown. So how to visualise the dodecahedron in Pymol or VMD? -- 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] why .top file is not updated with added waters in "gmx solvate" if customised water.gro is provided?
In the command gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21 -p dppc.top 768 waters are added, resulting in the "waterbox.gro". However, the "dppc.top" is not updated for its "[ molecules ]" section. I can of course manually add that. But why it is not automatically done? The prompt also shows "0" for "Number of SOL molecules": Generating solvent configuration Will generate new solvent configuration of 3x3x3 boxes Solvent box contains 4435 atoms in 4435 residues Removed 1235 solvent atoms due to solvent-solvent overlap Removed 1286 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: W ( 1 atoms): 768 residues Generated solvent containing 768 atoms in 768 residues Writing generated configuration to waterbox.gro Output configuration contains 2304 atoms in 896 residues Volume : 421.875 (nm^3) Density: 639.416 (g/l) Number of SOL molecules: 0 Processing topology Back Off! I just backed up dppc.top to ./#dppc.top.1# -- 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] How to use "define = -DPOSRES" in Gromacs 2018?
Thank you Mark! The "Protein_A.itp" is obtained by: python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb". So I should use "-r 1UBQ-CG.pdb"? So the whole command is the below? gmx grompp -p system.top -r 1UBQ-CG.pdb -c solvated.gro -f minimization.mdp -o minimization.tpr ------ Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 14, 2019 10:16 PM To: "gromacs.org_gmx-users"; Subject: Re: How to use "define = -DPOSRES" in Gromacs 2018? Thank you Mark! Sorry, I do not have a "targetcoords.gro" for the grompp. I was trying to use "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr", and the "system.top" has a line of " #include "Protein_A.itp" ", and the "Protein_A.itp" file has the restraints I need. Should I modify the "minimization.mdp" instead? -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 14, 2019 09:53 PM To: "gromacs.org_gmx-users"; Subject: How to use "define = -DPOSRES" in Gromacs 2018? My backbone restraints is shown in the "Protein_A.itp" file: #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC .. 1621POSRES_FCPOSRES_FCPOSRES_FC 1631POSRES_FCPOSRES_FCPOSRES_FC #endif The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file for "gmx grompp". However, adding "define = -DPOSRES" to the mdp file causes the error: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem for that? How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018? -- 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] How to use "define = -DPOSRES" in Gromacs 2018?
Thank you Mark! Sorry, I do not have a "targetcoords.gro" for the grompp. I was trying to use "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr", and the "system.top" has a line of " #include "Protein_A.itp" ", and the "Protein_A.itp" file has the restraints I need. Should I modify the "minimization.mdp" instead? -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 14, 2019 09:53 PM To: "gromacs.org_gmx-users"; Subject: How to use "define = -DPOSRES" in Gromacs 2018? My backbone restraints is shown in the "Protein_A.itp" file: #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC .. 1621POSRES_FCPOSRES_FCPOSRES_FC 1631POSRES_FCPOSRES_FCPOSRES_FC #endif The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file for "gmx grompp". However, adding "define = -DPOSRES" to the mdp file causes the error: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem for that? How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018? -- 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] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?
In Gromacs 2018, -r is used to provide the restraint file for grompp. I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro: gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o MD.tpr So in the command above, should I use AllAtom.pdb or CG.pdb as the file for "-r"? I tried both, and both can work without errors. But which one is more logically correct? I think the CG.pdb should definitely work. But why AllAtom.pdb is still okay? -- 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] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told "Too many LINCS warnings" in the minimization after solvation with coarse-grained waters. I try to diagnose the problems based on http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS warnings". Then I looked at the edr files. The potential in "emtol = 1000" and "emtol = 100" runs were actually converging https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png My understanding for the "LINCS warnings" is, the system is not stable. But why the potential is still converging? Do I need to adjust the "lincs warning threshold", or "set the environment variable GMX_MAXCONSTRWARN to -1"? How to do that? Is there a "standard" mdp file for minimization for a coarse-grained system with 10 proteins in water? I am using this, but I do not know how to modify it. https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 22, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told "Too many LINCS warnings" in the minimization after solvation with coarse-grained waters. I try to diagnose the problems based on http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
Dear Fotis and Peter, Thank you very much for the help. Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do that? I think my problem is not the first reason (i.e. something wrong with the system structure or topology), because the potential is decreasing for the minimization step after inserting 10 protein molecules https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization%20after%20insert%2010%20proteins.jpg $ Steepest Descents converged to machine precision in 4251 steps, $ but did not reach the requested Fmax < 1. $ Potential Energy = -2.4130119e+05 $ Maximum force = 9.1535597e+00 on atom 2335 $ Norm of force = 7.1063030e-01 Peter, how to replace all constraints for stiff bonds? -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 22, 2019 05:58 AM To: "gromacs.org_gmx-users"; Subject: Re: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS warnings". Then I looked at the edr files. The potential in "emtol = 1000" and "emtol = 100" runs were actually converging https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png My understanding for the "LINCS warnings" is, the system is not stable. But why the potential is still converging? Do I need to adjust the "lincs warning threshold", or "set the environment variable GMX_MAXCONSTRWARN to -1"? How to do that? Is there a "standard" mdp file for minimization for a coarse-grained system with 10 proteins in water? I am using this, but I do not know how to modify it. https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 22, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told "Too many LINCS warnings" in the minimization after solvation with coarse-grained waters. I try to diagnose the problems based on http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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] How to install a new force-field?
Thank you very much! I got it now! Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:54 PM To: "gromacs.org_gmx-users"; Subject: Re: How to install a new force-field? Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as shown on http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs I want to make sure the CHARMM36m is used instead of CHARMM36. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:38 PM To: "gromacs.org_gmx-users"; Subject: How to install a new force-field? Dear Gromacs users, In the pdb2gmx command, we are asked to select the force field to simulate our protein system. I am told that a99SB-disp and CHARMM36m are better force-field for the proteins. But both of them are not the default ones. Can I ask 1) What is the latest officical website to download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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] How to install a new force-field?
Dear Gromacs users, In the pdb2gmx command, we are asked to select the force field to simulate our protein system. I am told that a99SB-disp and CHARMM36m are better force-field for the proteins. But both of them are not the default ones. Can I ask 1) What is the latest officical website to download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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] How to install a new force-field?
Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as shown on http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs I want to make sure the CHARMM36m is used instead of CHARMM36. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:38 PM To: "gromacs.org_gmx-users"; Subject: How to install a new force-field? Dear Gromacs users, In the pdb2gmx command, we are asked to select the force field to simulate our protein system. I am told that a99SB-disp and CHARMM36m are better force-field for the proteins. But both of them are not the default ones. Can I ask 1) What is the latest officical website to download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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.
