[gmx-users] Trajectory to matrix
Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 In the rows I'd like to put z coordinate changing in time. Any suggestion? Thanks-- 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] do_dssp segmentation fault
Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Thank in ad-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp segmentation fault
On 22/11/2011 7:28 PM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Make sure you have followed all the instructions available with do_dssp -h, and that your DSSP is the old version, not the updated one. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trajectory to matrix
On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 That will be your job to parse the .gro file suitably and write a header. In the rows I'd like to put z coordinate changing in time. g_traj -xvg none is the place to start. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trajectory to matrix
Where can I download the old version? Thanks Da: Mark Abraham mark.abra...@anu.edu.au A: Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Martedì 22 Novembre 2011 9:32 Oggetto: Re: [gmx-users] Trajectory to matrix On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 That will be your job to parse the .gro file suitably and write a header. In the rows I'd like to put z coordinate changing in time. g_traj -xvg none is the place to start. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Force equations of virtual site type 4fdn
Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? Appreciate any help and thanks in advance! 2011-11-22 Best wishes！ Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force equations of virtual site type 4fdn
On 22/11/2011 7:27 PM, xuji wrote: Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? You will have seen that the manual also says: The force on particles i, j, k and l due to the force on the virtual site are computed through chain rule derivatives of the construction expression. This is exact and conserves energy, but it does lead to relatively lengthy expressions that we do not include here (over 200 floating-point operations). The interested reader can look at the source code in vsite.c. Perhaps you should try this. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER
Hi there, Acpype does the conversion for you and the results from their own testing are here: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx For reproducing experimental data I would look in the original force-field publications. Oliver On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts mrshi...@gmail.com wrote: Is anyone aware of any benchmark analysis about the implementation of the amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in GROMACS and AMBER. I am interested to know in what extend the energies correlate and if the results agree with experimental data. Whether the results compare agree with experimental data is irrelevant to the correctness of the implementation -- that has to do with the validity of AMBER99sb to begin with. The only question is, do GROMACS and AMBER give the same energies for the same configurations? I actually do not know the answer, and would be interested to hear if it's been tested. http://ffamber.cnsm.csulb.edu/ does not appear to have the very comprehensive tests that appear for earlier models at the current time. I SUSPECT there should not be a problem, since AMBER99sb just changed a couple of torsions, so errors are unlikely (though in theory possible). -- 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] PMF curve
Hello, I have done umbrella sampling for 10ns on 23 windows and g_wham program shows converged histograms and PMF curve. I used the following g_wham command, g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -o profile.xvg -hist histo.xvg -b 1000 -e 1 I considered first 1ns simulation as equilibration. when I change the -b from 1000 to 1500, 2000... I can still get converged PMF curve but the PMF convergence is achieved at different places, for eg, when I increase -b the PMF converges at -18, -17, -16. and g_wham do not show any warning for poor sampling. Is there any problem with the sampling windows when I increase the -b? or simply we can select the PMF curve as obtained wtih -b 1000? Regards, Vijay. -- 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] PMF curve
Hello, I got a PMF curve like 0...-2...022. its converged at 22. I have a doubt in the final deltaG value, for this curve the deltaG is 22-2 or 22-0. Regards, Vijay. -- 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] Box in Implicit Solvent Simulations
Hi, I am running simulations using implicit solvent. I am using the pbc = no option in my mdp file, however, I see it the .gro file that gromacs is creating a box for the system.What is the effect of the box in implicit solvent simulations? This is the mdp file that I am using: --run.mdp-- integrator = md nsteps = 2 dt = 0.001 implicit_solvent = GBSA pbc = no nstlist = 0 ns_type = simple rlist = 0 rgbradii = 0 coulombtype = Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 1000 energygrps = Protein_chain_A Protein_chain_C Protein_chain_E Protein_chain_G Protein_chain_I Protein_chain_K gen_vel = yes gen_temp = 1000 ld_seed = -1 gen_seed = -1 nstxout = 1 nstvout = 1 nstxtcout = 1 nstenergy = 1 -- Thanks, Ifat M.Sc. Student Bar Ilan University Ramat Gan Israel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box in Implicit Solvent Simulations
On 22/11/2011 10:08 PM, ifat shub wrote: Hi, I am running simulations using implicit solvent. I am using the pbc = no option in my mdp file, however, I see it the .gro file that gromacs is creating a box for the system.What is the effect of the box in implicit solvent simulations? None, if pbc = no. When writing a .gro file some data has to go into the space the format allows for the box. However the .mdp file controls whether that is significant. Later on when using analysis tools, some of the analyses might erroneously use that box if you don't give suitable instructions not to. Mark This is the mdp file that I am using: --run.mdp-- integrator = md nsteps = 2 dt = 0.001 implicit_solvent = GBSA pbc = no nstlist = 0 ns_type = simple rlist = 0 rgbradii = 0 coulombtype = Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 1000 energygrps = Protein_chain_A Protein_chain_C Protein_chain_E Protein_chain_G Protein_chain_I Protein_chain_K gen_vel = yes gen_temp = 1000 ld_seed = -1 gen_seed = -1 nstxout = 1 nstvout = 1 nstxtcout = 1 nstenergy = 1 -- Thanks, Ifat M.Sc. Student Bar Ilan University Ramat Gan Israel -- 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] Rv: g_helixorient question
Hi, I'm sorry to insist in my question but if somebody could answer or just to send me some information or place to look for, I will be very thanked. GROMACS manual does not give any information but the way to use it. Nothing about the contain of files. Thanks again. - Mensaje reenviado - De: Javier Romero Garcia kurcol...@yahoo.com Para: gmx-users@gromacs.org gmx-users@gromacs.org Enviado: lunes 21 de noviembre de 2011 10:44 Asunto: g_helixorient question Hello! My name's Javier Romero and I am a PhD student, writting from Barcelona. I am simulating an anphipatic helix of 23 residues, in the interface of a DPPC membrane and water. I am trying to measure the rotation of the helix using the tool g_helixorient. Could be somebody so kind to explain me the meaning of each kind of the files? I mean: - Twist. - Tilt. - Tetha. - Rotation. - Rise. - Radius. - Helixaxis. - Center. - Bending. Thanks in advance.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Rv: g_helixorient question
On 22/11/2011 10:41 PM, Javier Romero Garcia wrote: Hi, I'm sorry to insist in my question but if somebody could answer or just to send me some information or place to look for, I will be very thanked. I imagine that these kinds of definitions are discussed in general texts on (computational or experimental) modelling of proteins, so that may be a good place to start with understanding what g_helixorient might be calculating. GROMACS manual does not give any information but the way to use it. Nothing about the contain of files. g_helixorient -h has some very basic information that could help. Otherwise, I'm sure the GROMACS team regret that the documentation is a bit lacking. Please do remember that GROMACS is a volunteer effort. Because our resources are finite, it won't always be able to be what we would all like it to be. The existence of the g_helixorient tool is already rather more than you paid for, too ;-). Do consider using other simulation packages' analysis tool sets - often trajectories can be inter-converted with little fuss. In extremis, please consider reading the code of src/tools/gmx_helixorient.c - but you'll need to be unafraid of the mathematics of 3D rotation! Mark Thanks again. - Mensaje reenviado - *De:* Javier Romero Garcia kurcol...@yahoo.com *Para:* gmx-users@gromacs.org gmx-users@gromacs.org *Enviado:* lunes 21 de noviembre de 2011 10:44 *Asunto:* g_helixorient question Hello! My name's Javier Romero and I am a PhD student, writting from Barcelona. I am simulating an anphipatic helix of 23 residues, in the interface of a DPPC membrane and water. I am trying to measure the rotation of the helix using the tool g_helixorient. Could be somebody so kind to explain me the meaning of each kind of the files? I mean: - Twist. - Tilt. - Tetha. - Rotation. - Rise. - Radius. - Helixaxis. - Center. - Bending. Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding Dimer calculations
Dear all, Could anybody suggest me how to do dimer calculation using gromacs or guide me to some paper or journal that describes the same. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding Dimer calculations
On 22/11/2011 11:06 PM, Ravi Kumar Venkatraman wrote: Dear all, Could anybody suggest me how to do dimer calculation using gromacs or guide me to some paper or journal that describes the same. The same considerations apply - simulation design depends on what you wish to observe. For a dimer, you may be able to get away with using the same [moleculetype] for each molecule. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp segmentation fault
Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- 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] Cavity detection on membrane protein surface
Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification process? Thanks in adavance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cavity detection on membrane protein surface
On 23/11/2011 12:33 AM, Alex Jemulin wrote: Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification process? g_rms can fit based on the whole protein and measure the RMS deviation based on just a subset of the protein. So I suggest making a large number of groups that appeal to you and scripting g_rms to loop through them. http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts may help. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] -ter flag, pdb2gmx
Dear gmx-users, I'm having some problems using the flag -ter of pdb2gmx. The syntax I'm using is the following, for a protein dimer: pdb2gmx -f protein_dimer.pdb -o start.gro -p start.top -ter Instead of prompting a menu with the choice of different chemical groups, the flag is ignored by gromacs, which creates the ouput files as usual. What I'm attempting to do is to create a C-terminus without a carboxylic group. Best regards Alberto -- 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 obtain NOEs from MD trajectory ?
Dear Gromacs users, Is there any algorithm/procedure to calculate NOEs from an MD trajectory? I'd greatly appreciate any references where the algorithm is described. Best regards, Jose M. Borreguero -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)
When GROMACS takes care of the optimization this doesn't happen. Jose R Tusell On Tue, Nov 22, 2011 at 12:35 AM, Gerrit Groenhof ggro...@gwdg.de wrote: On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote: gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Does anyone know what is going on with the coordinates of the QM region? Why are they not converted to the correct units? Could anyone point me to the error? I have not experienced this myself. The only thing I can think of is that ORCA returns the atom coordinates in nm? Does this happen also when you let Gromacs take care of the optimization? Gerrit -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)
Dear Jose, Also our calculations using bOpt with ORCA are fine. ORCA does not give the coordinates in nm, but in Angstrom. Which version of gromacs are you using? Christoph On 11/22/2011 03:53 PM, Jose Tusell wrote: When GROMACS takes care of the optimization this doesn't happen. Jose R Tusell On Tue, Nov 22, 2011 at 12:35 AM, Gerrit Groenhofggro...@gwdg.de wrote: On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote: gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Does anyone know what is going on with the coordinates of the QM region? Why are they not converted to the correct units? Could anyone point me to the error? I have not experienced this myself. The only thing I can think of is that ORCA returns the atom coordinates in nm? Does this happen also when you let Gromacs take care of the optimization? Gerrit -- 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] Charged tube
Dear Gmx Users, I am wondering whether you know any software which allows to build a charged tube with specified dimensions which will work with Gromacs? Is it possible to add charges or e.g. add ions and use position restrained dynamics? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pyroglutamate in gromos53a6
Dear all, Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) ? Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a way I could adapt these to gromos53a6.ff? Can I use, for example, the gromos53a6.ff atom types from glutamine, add/remove appropriate bonds / angles / impropers and then take the corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume that what I've just suggested is the cowboy method and that in reality it is not that straightforward, right? Kind regards, Henry Henry Hocking, PhD Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht, The Netherlands Phone: +31-30-2532875 Fax: +31-30-253 7623 E-mail: h.g.hock...@uu.nl -- 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] SASA query
Hi Gromacs Users I have a query regarding g_sas which i intend to use for my MM/PBSA calcualtion i am planing to use g_sas for calculating the SASA using a probe radius of 0.14 nm is this okay ? o secondly ∆Gsolv,np = 0.00542*SASA + 0.92 is this master equation right third and important (1) first i calculate for PTN+water and get the SASA for protein (2 ) i calculate for LIgand +water and get the SAS for Ligand (3) I calculate Ptn+ligand+water and choose PTN+LIgand and get the SASA for P+ L right ??? (4) and the final SASA as *(Delta SASA)=SASA(protein)+SASA(ligand)-SASA(protein+ligand)** is this the right procedure. R.S.K.Vijayan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pyroglutamate in gromos53a6
Hi Henry, That would be a bit of a wild west approach. A better approximation would be taking the charges from the backbone amide group, as it is just an amide with on either side aliphatic carbons. Doing it properly is a bit more involved, as for the G53a6 FF you need to choose parameters giving the right free enthalpy of solvation. Groetjes, Tsjerk On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking h.g.hock...@uu.nl wrote: Dear all, Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) ? Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a way I could adapt these to gromos53a6.ff? Can I use, for example, the gromos53a6.ff atom types from glutamine, add/remove appropriate bonds / angles / impropers and then take the corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume that what I've just suggested is the cowboy method and that in reality it is not that straightforward, right? Kind regards, Henry Henry Hocking, PhD Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht, The Netherlands Phone: +31-30-2532875 Fax: +31-30-253 7623 E-mail: h.g.hock...@uu.nl -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain NOEs from MD trajectory ?
Hi Jose, Check g_rmsdist -h Not sure about the references though. Cheers, Tsjerk On Nov 22, 2011 3:23 PM, Jose Borreguero borregu...@gmail.com wrote: Dear Gromacs users, Is there any algorithm/procedure to calculate NOEs from an MD trajectory? I'd greatly appreciate any references where the algorithm is described. Best regards, Jose M. Borreguero -- 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] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs
Greetings Gromacs Users, I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides. (The residue names do change appropriately i.e., CYS becomes CYS2.) The disulfides do form correctly when using the other currently available FFs. All the output shown below my message is from running GROMACS-4.5.5. Note the same thing happens when running GROMACS-4.5.3 and GROMACS-4.0.5. I have not found any discussion of this issue on the internet (in general) or the gmx mailing list (specifically), however I suspect this may have contributed to at least one user message ( http://lists.gromacs.org/pipermail/gmx-users/2011-March/059242.html ). It is trivial to fill in the missing bond, angle, and dihedral types by hand after running pdb2gmx (this may be why this has not been discussed too much), but I am interested in figuring out a long term solution because the lab I work in has developed a FF which uses the GROMOS bonds and angles (and thus also uses the same format as GROMOS does for the ffbonded.itp file). We hope to have our FF supported by GROMACS in the future, but we want to make sure that GROMACS users would not encounter this problem if they selected our FF. Could anyone point me in the right direction? Thanks for your consideration of this! All the best, Elizabeth A. Ploetz Kansas State University The list below shows the tested FFs. A '+' indicates proper disulfide description in the topology file, and an 'X' indicates the output contained missing bond/angle/dihedral types. Test of disulfide bond formation using pdb2gmx and FFs available in GROMACS-4.5.5: + 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 (with CMAP) - version 2.0 X 9: GROMOS96 43a1 force field X10: GROMOS96 43a2 force field (improved alkane dihedrals) X11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) X12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) X13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) +14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) +15: [DEPRECATED] Encad all-atom force field, using full solvent charges +16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges +17: [DEPRECATED] Gromacs force field (see manual) +18: [DEPRECATED] Gromacs force field with hydrogens for NMR This is an example of how I ran pdb2gmx: :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.5.5 (-: . . skipping . 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 (with CMAP) - version 2.0 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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended simple point charge 3: None 1 Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading ../start.pdb... Read
[gmx-users] Folding of small globular peptide
Dear Gromacs Users! I want to simulate folding of small globular protein in water. I have linear structure ( with all psi\ phi torsions set to 180 ) of my peptide made in HyperChem as well as NMR structure ( for control ). Could you tell me what specificities of such simmulation should I take into account ? Could I use parametets from Lyzocyme tutorial for NPT NVT and MD simulation? What average length of the run trajectory should be if my peptide 1) is the simple coil? 2) Has secondary structure- e.g consist of 2 short helicees and one b-sheet Thanks, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs
Hi Elizabeth, These missing terms are filled in automatically by grompp from the bondtypes, angletypes and dihedraltypes definitions in the *bon.itp. Unless grompp complains about missing terms, you'll be fine. You can check whether everything is okay by writing out a processed topology (grompp -pp) and looking up the bonds.angles/dihedrals there. Cheers, Tsjerk On Wed, Nov 23, 2011 at 12:32 AM, Elizabeth Ploetz plo...@ksu.edu wrote: Greetings Gromacs Users, I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides. (The residue names do change appropriately i.e., CYS becomes CYS2.) The disulfides do form correctly when using the other currently available FFs. All the output shown below my message is from running GROMACS-4.5.5. Note the same thing happens when running GROMACS-4.5.3 and GROMACS-4.0.5. I have not found any discussion of this issue on the internet (in general) or the gmx mailing list (specifically), however I suspect this may have contributed to at least one user message ( http://lists.gromacs.org/pipermail/gmx-users/2011-March/059242.html ). It is trivial to fill in the missing bond, angle, and dihedral types by hand after running pdb2gmx (this may be why this has not been discussed too much), but I am interested in figuring out a long term solution because the lab I work in has developed a FF which uses the GROMOS bonds and angles (and thus also uses the same format as GROMOS does for the ffbonded.itp file). We hope to have our FF supported by GROMACS in the future, but we want to make sure that GROMACS users would not encounter this problem if they selected our FF. Could anyone point me in the right direction? Thanks for your consideration of this! All the best, Elizabeth A. Ploetz Kansas State University The list below shows the tested FFs. A '+' indicates proper disulfide description in the topology file, and an 'X' indicates the output contained missing bond/angle/dihedral types. Test of disulfide bond formation using pdb2gmx and FFs available in GROMACS-4.5.5: + 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 (with CMAP) - version 2.0 X 9: GROMOS96 43a1 force field X10: GROMOS96 43a2 force field (improved alkane dihedrals) X11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) X12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) X13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) +14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) +15: [DEPRECATED] Encad all-atom force field, using full solvent charges +16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges +17: [DEPRECATED] Gromacs force field (see manual) +18: [DEPRECATED] Gromacs force field with hydrogens for NMR This is an example of how I ran pdb2gmx: :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.5.5 (-: . . skipping . 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 (with CMAP) - version 2.0 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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
