[gmx-users] GPU-gromacs
Dear prof., i want install gromacs on a multi-core workstation with a GPU(tesla c2075), should i install the openmpi or mpich2? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 113, Issue 108
Dear prof. The format of parameters is convenient to the software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to the itp format for gromacs. so i use acpype to get itp format. i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor. it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ? At 2013-09-24 18:00:04,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: Charmm 36 forcefield with verlet cut-off scheme (Justin Lemkul) 2. Re: The charge of cofactor and ligand (Justin Lemkul) 3. Re: Fatal Error: Residue 'DMP' not found in residue topology database (Santhosh Kumar Nagarajan) 4. Re: Regarding g_sgangle index file (Venkat Reddy) -- Message: 1 Date: Mon, 23 Sep 2013 21:25:19 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5240e9ff.1020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/23/13 4:04 PM, akk5r wrote: With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet rvdw-switch has no effect here, and I have no real hard evidence to know whether or not this will produce the same effect as the traditional settings. You would have to carefully demonstrate that what you're doing doesn't break the force field. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Message: 2 Date: Mon, 23 Sep 2013 21:26:15 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] The charge of cofactor and ligand To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5240ea37.4090...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 9/23/13 5:10 PM, aixintiankong wrote: Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype i ben.mol2 c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? Why not just use the parameters that are already published? Unless there's something wrong with them, there's no need to reinvent the wheel. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Message: 3 Date: Mon, 23 Sep 2013 20:43:28 -0700 (PDT) From: Santhosh Kumar Nagarajan santhoshraja...@gmail.com Subject: [gmx-users] Re: Fatal Error: Residue 'DMP' not found in residue topology database To: gmx-users@gromacs.org Message-ID: 1379994208045-5011420.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Justin.. I understand the problem.. But.. How to generate a .rtp file myself.. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333p5011420.html Sent from the GROMACS Users Forum mailing list
[gmx-users] The charge of cofactor and ligand
Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 113, Issue 106
Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge formhttp://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype –i ben.mol2 –c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? At 2013-09-24 02:24:20,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: The charge of cofactor and ligand (Mark Abraham) 2. Re: Regarding g_sgangle index file (Teemu Murtola) 3. g_energy (Marcelo Vanean) 4. Re: confusion about implicint solvent (Szil?rd P?ll) 5. Re: Re: Charmm 36 forcefield with verlet cut-off scheme (Justin Lemkul) 6. Re: script to convert the TIP3P water model into TIP4(P)/2005 (Justin Lemkul) 7. Re: confusion about implicint solvent (Justin Lemkul) -- Message: 1 Date: Mon, 23 Sep 2013 19:40:23 +0200 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] The charge of cofactor and ligand To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumat5bsq5xzr-q0zu27bt0hma2m9wauduf-6lk+dn1ss...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote: Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 113, Issue 54
Dear prof. after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start form 1 not the 20. how can i change the order of residue? Thank you very much! At 2013-09-12 18:00:06,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RE: average pressure of a system (Dwey Kauffman) 2. how to make a index file (aixintiankong) 3. RE: RE: average pressure of a system (Dallas Warren) 4. Re: RE: average pressure of a system (Tsjerk Wassenaar) 5. PhD vacancy on MD modelling at University of Groningen (Patrick Onck) -- Message: 1 Date: Wed, 11 Sep 2013 20:31:50 -0700 (PDT) From: Dwey Kauffman mpi...@gmail.com Subject: [gmx-users] RE: average pressure of a system To: gmx-users@gromacs.org Message-ID: 1378956710192-5011137.p...@n6.nabble.com Content-Type: text/plain; charset=UTF-8 Justin Lemkul wrote On 9/11/13 12:12 AM, Dwey Kauffman wrote: True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has millions or trillions. Pressure fluctuations decrease on the order of sqrt(N), so the system size itself is a determining factor for the pressure fluctuations. As previous discussions have rightly concluded, pressure is a somewhat ill-defined quantity in molecular systems like these. Dose it also imply that it is not a good idea to study the relationship between dimer (multimer) dissociation and macroscopic pressure in this case ? (due to the ill defined pressure). I would simply think it would be very hard to draw any meaningful conclusions if they depend on a microscopic quantity that varies so strongly. It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8, 0.9, 1.0, 1.1, 1.2 , perform independent simulations, and then obtain outcomes of targeted quantities for comparison. As with the original issue, I would find it hard to believe that any of the differences observed in such a setup would be meaningful. Is 0.7 ± 100 actually different from 1.2 ± 100? You could try altering tau_p, but I doubt there is any value in doing so. I would give it a try. This will really only change the relaxation time. Smaller values of tau_p may improve the average slightly, but may also (more likely) lead to instability, especially with Parrinello-Rahman. I carried out independent NPT processes with different tau_p values = 1.5, 1.0 and 0.5 ## tau_p 1.5 Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.628592.6 185.682.67572 (bar) ## tau_p 1.0 Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.8867691.7187.737 0.739 (bar) ## tau_p 0.5 Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.399112.2185.708 6.8189 (bar) ## It is clear that when tau_p =1.0, average pressure of the system (=0.89 bar) is close to ref_p =1.0 bar However, it is unclear to me as to how to assign a good value to tau_p in order to reach at a close value of ref_p. As shown above, both of the average pressures as tau_p =1.5 and 0.5 are much higher than that as tau_p =1.0. A smaller tau_p may or may not help. Another issue caused by system pressure is about pbc box size. Since I use pressure coupling, the box size is not fixed such that protein moved away the center of membrane for a long simulation like 30 ns. Box size changes significantly during production MD. Is there a way to fix the box size at the very beginning ? although turning off pressure coupling will make box size fixed. Best regards, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011137.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date
[gmx-users] how to make a index file
i want to analyze the change of secondary structure of the mainchian frome residue 20 to residue 60. so i want to make a index file that only contain the maninchian+H from residue 20 to residue 60. i have inputed the command make_ndx -f em.pdb -o index.ndx, but i don't kown how to do next . what should i input ? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g__dist calculate the distance of two residues from different loops
Dear， when i keep the ligand in the active site, I use the g_dist calculate the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residues. after using g_dist calculate the distance, i look the distance.xvg file and find that the |d|=0. why? In the pymol i can look the gap, but the distance.xvg show the |d|=0. when i remove the ligand and get the md.xtc, i calculate the distance between the two residues the |d|1nm. so i think the ligand can control the Channels opend, this is right or not ? And i only want to show teh |d| lines in the distance.xvg, how can i carry out it ?-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to describe the change of channel in the MD
Dear, In the MD, I find that when the ligand keep in the active site , the channel formed by two loops is closed. without the ligand the channel is opened. I don't know how to describe the change of channel. could i describe the channel by calculating the the most narrow distance(mass center) between the residues on the two loops? please give me some adviece. thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to describe the change of channel in the MD
Dear, In the MD, I find that when the ligand keep in the active site , the channel formed by two loops is closed. without the ligand the channel is opened. I don't know how to describe the change of channel. could i describe the channel by calculating the the most narrow distance(mass center) between the residues on the two loops? please give me some adviece. thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] simulate a protein covalently binding with a organic molecule
Dear, Please help me . i want to simulate a systme of the protein covalently bind with a organic molecule. Part of the model is standard resides and the rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i don't know how to get the topology of the model. wait for you help thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] simulate a protein covalently binding with a organic molecule
Dear, Please help me . i want to simulate a systme of the protein covalently bind with a organic molecule. Part of the model is standard resides and the rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i don't know how to get the topology of the model. wait for you help thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be
i want to study how ligands change the conformations using the gromacs software and i want to run 100ns, but i don't konw how to reasonably set the nstxout nstvout nstenergy nstlog and nstxtcout. Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be
Dear, i want to study how ligands change the conformations using the gromacs software and i want to run 100ns, but i don't konw how to reasonably set the nstxout nstvout nstenergy nstlog and nstxtcout. Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about command do_dssp
Dear prof. i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein. when i perform the do_dssp and select MainChain , the fatal erros come out as follow; Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) it is means thant i don't install do_dssp? however, when i perform the which do_dssp at the terminal, the termianl output /usr/local/gromacs-4.6.1/bin/do_dssp. i don't know where is wrong. should i reset the environment of the do_dssp? please help me ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to build the loop of protein model
Dear, In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model thant the ligand is in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a protein structure without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and sturctue the the RMSD bettwen the two protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit,but the loop of protein is disordered. can i use the Homology modeling ,docking or just use pymol extract the NAD+ and ligand from the complex and the put them into the protein with the disoreded loop ? And then to make a MD. In order to make the disordered into the helix using gromacs, how long should i run the MD and what is the value of dt , 0.001 or 0.002? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] using CHARMM force field for organic molecule
Dear , I want to use charmm force field to simulate the protein and ligand system. The protein can selcet charmm27 in gromacs, but i don't konw how to get the charmm force field for the ligand. could tell me a simple way to get the to Topology file for the organic molecule . thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] align the 1000 frames from MD.xtc
Dear, i have extracted 1000 frames from MD.xtc file. i found the relative postion of them is very diffrent . so i want to align them and keep them . please help me thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] keeping the position and coordinates at the same when extarct frames
Dear, After extracting the frames of the steep 20th pdb file and 993th pdb file from the MD, i found the position of the two frames are very diffrent in pymol and vmd. why? could i exracting pdb file form different steeps and keep them in align? please help me . thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] extracting the multiple frames (pdb files) in align
Dear, After extracting the frames of the steep 20th pdb file and 993th pdb file from the MD, i found the position of the two frames are very diffrent in pymol and vmd. why? could i exracting pdb file form different steeps and keep them in align? please help me . thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 108, Issue 130
Dear, could you tell me more detailed about to extract frames from a MD to align. i try the follow command,but it does not work, trjconv -s topol.tpr -f traj.xtc -skip 10 -pbc nojump -sep. could you tell me how to align all the frames with the first pdb file that was extracted from traj.xtc ? thank you for you help! On 4/21/13 7:40 AM, aixintiankong wrote: Dear, i have extracted 1000 frames from MD.xtc file. i found the relative postion of them is very diffrent . so i want to align them and keep them . please help me Please read trjconv -h. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:Re:gmx-users Digest, Vol 108, Issue 130
Dear Justin, i really need you help and i will wait for your help ! i am a newer and there anyone can help me , i hope the frames extracted from a MD can align. i really don't know why this happen. thank you very much! At 2013-04-21 21:47:36,aixintiankong aixintiank...@126.com wrote: Dear, could you tell me more detailed about to extract frames from a MD to align. i try the follow command,but it does not work, trjconv -s topol.tpr -f traj.xtc -skip 10 -pbc nojump -sep. could you tell me how to align all the frames with the first pdb file that was extracted from traj.xtc ? thank you for you help! On 4/21/13 7:40 AM, aixintiankong wrote: Dear, i have extracted 1000 frames from MD.xtc file. i found the relative postion of them is very diffrent . so i want to align them and keep them . please help me Please read trjconv -h. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 108, Issue 130
Dear Justin, i really need you help and i will wait for your help ! thank you very much! At 2013-04-21 21:47:36,aixintiankong aixintiank...@126.com wrote: Dear, could you tell me more detailed about to extract frames from a MD to align. i try the follow command,but it does not work, trjconv -s topol.tpr -f traj.xtc -skip 10 -pbc nojump -sep. could you tell me how to align all the frames with the first pdb file that was extracted from traj.xtc ? thank you for you help! On 4/21/13 7:40 AM, aixintiankong wrote: Dear, i have extracted 1000 frames from MD.xtc file. i found the relative postion of them is very diffrent . so i want to align them and keep them . please help me Please read trjconv -h. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to extract individual frames from trajectory
At 2013-04-14 11:07:39,aixintiankong aixintiank...@126.com wrote: Dear, I have made a 10ns prodution MD, I want to extract frames from the molecular dynamics simulations at regular intervals of 10ps and keep the file as individual pdb file. The dt=0.002，nstxtcout = 500，i want to use the follow command , trjconv -s topol.tpr -f traj.xtc -skip (number) -o conf.pdb -sep but i don't now how to set the number of skip,please help me. thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to use the trjconv -sep and -skip to get the individual file
Dear, I have made a 10ns prodution MD, The set dt=0.002，nstxtcout = 500 in mdp file. I have made 10ns prodution MD, I want to extract frames from the molecular dynamics simulations at regular intervals of 10ps and keep the file as individual pdb file i want to use the follow command , trjconv -s topol.tpr -f traj.xtc -skip (number) -o conf.pdb -sep but i don't now how to set the number of skip,please help me and tell me what the skip mean thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to simulate the transformation of loop
Dear, In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. i don't know how to the simulate the state of the shape of the loop at the different the situation. During the simulation, should i set the specific parameters in the mdp , such as temperature or the others please give me some advice .thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to extract individual frames from trajectory
Dear, I have made a 75ns prodution MD, I want to extract frames from the molecular dynamics simulations at regular intervals of 10ps and keep the file as individual pdb file. i want get many individual pdb files. colud anyone can tell me how to perform the command? thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to split the disulfide bonds in CYSH?
Dear, In my system ,there are many disulfide bonds in my protein. i want to split these disulfide bonds to CYSH. I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top -water spce -ss ,but i get the CYS2. please help me ,thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MD stop,systme not equilibrium
Dear, when i make MD of my system, i set the MD stop ater 3ns. however, when the gromacs stop , i find that the system of protein and ligand is not equilibrium, i want to continue the process to 5ns. but i don't konw how to do this.please help me. thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to install the gromacs 4.6.1 using the intel icc and ifor
Dear, I have install intel icc and ifor on my system centos, and i want to install gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use to indicate the icc and ifor when i install the gromacs. thank you very much! At 2013-02-21 13:00:55,aixintiankong aixintiank...@126.com wrote: Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters exchange with the solvent waters, how to constrain solvent waters adding in active site when i solvate protein and diffusing in active site during diffuse dynamic simulation. can i set some parameters in mdp file to slove the problem? Forwarding messages From: aixintiankong aixintiank...@126.com Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fw:some waters in active site of receptor
Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not? Forwarding messages From: aixintiankong aixintiank...@126.com Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] implicit solvent
Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not? At 2013-03-02 21:21:38,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Fw:some waters in active site of receptor (aixintiankong) 2. Re: removing number of sol (gromacs query) 3. Semiisotropic pressure coupling problem (congchen) -- Message: 1 Date: Sat, 2 Mar 2013 18:59:27 +0800 (CST) From: aixintiankong aixintiank...@126.com Subject: [gmx-users] Fw:some waters in active site of receptor To: gmx-users@gromacs.org Message-ID: 625c04ca.1a6bf.13d2ac1a871.coremail.aixintiank...@126.com Content-Type: text/plain; charset=GBK Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not? Forwarding messages From: aixintiankong aixintiank...@126.com Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- Message: 2 Date: Sat, 2 Mar 2013 15:01:25 +0200 From: gromacs query gromacsqu...@gmail.com Subject: Re: [gmx-users] removing number of sol To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAPe3FJD4s+Y9KZUPpT_FNRLdUCOpdH-WJS=jmrdgrzsfthq...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Erik, I am new to Gromacs and used AMBER before, and I am exploring various options in GROMACS too. Surely I will look in to g_select. Also as I was using sed, one should include an extra space (using vi) in gro file just before residue number and then can use sed to remove like this: sed -e '/ 35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro new2.gro But please note I included an extra space / 35SOL/d (instead of /35SOL/d) by this sed will remove 35SOL not 135SOL. regards, On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Then the problem lies in automating what molecules are to be removed, right? Try g_select or look into trjorder. Erik On Mar 1, 2013, at 2:45 PM, gromacs query wrote: Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed) regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote
[gmx-users] Fw:some waters in active site of receptor
Forwarding messages From: aixintiankong aixintiank...@126.com Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
