[gmx-users] my big problem
Hi everybody, I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error : Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 7 additional processes aborted (not shown) I only can think about the difference may be caused because of my protein -ligand complex is very big.It has 2 chains. After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy, nstxtcoutvalues than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics.Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files? thank you .. - Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] my big problem
? wrote: Hi everybody, I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error : Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 7 additional processes aborted (not shown) This is just a generic MPI error message. You haven't established what has caused it yet. Try running the system for a short time on a single processor, to eliminate parallelism as a source of the problems (you'll need to re-grompp, of course). I only can think about the difference may be caused because of my protein -ligand complex is very big.It has 2 chains. After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy, nstxtcoutvalues than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics. Probably your topology is broken or your structure is insufficiently minimized or equilibrated. Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files? We can't tell yet, since you haven't told us any symptoms that are useful diagnostically. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] my big problem
Hi Ozge, Mark, Mark is of course completely right regarding the MPI error.., you're messing up something. Where was my mind? Sharp peaks in the RMSD and radius of gyration plots may indicate jumps over the periodic boundaries. But, that should not be a cause for breaking a simulation. The only parameter you mentioned that could be linked to the stability of the simulation is the nstcomm, the others only control output. Of course you should try to understand what made your simulation crash, in stead of treating symptoms, possibly covering up some flaw in the set up of the simulation. Check the .log file. Tsjerk On 3/29/07, Mark Abraham [EMAIL PROTECTED] wrote: ? wrote: Hi everybody, I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error : Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 7 additional processes aborted (not shown) This is just a generic MPI error message. You haven't established what has caused it yet. Try running the system for a short time on a single processor, to eliminate parallelism as a source of the problems (you'll need to re-grompp, of course). I only can think about the difference may be caused because of my protein -ligand complex is very big.It has 2 chains. After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy, nstxtcoutvalues than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics. Probably your topology is broken or your structure is insufficiently minimized or equilibrated. Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files? We can't tell yet, since you haven't told us any symptoms that are useful diagnostically. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] my big problem
Hi Mark, Apparently, my mind was strongly biased towards reports on RMSD radius of gyration sharp peaks, ignoring too much of what went before started to run. I fully agree that I was careless here. But he seems to say he did a simulation of 20 ns and then wonders why the RMSD plots are different. Hasn't heard of stochastic processes. In any case, having a two-component system with sharp peaks in RMSD and RGYR does indicate PBC jumps, though that doesn't justify my neglect of the other matters. Tsjerk On 3/29/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Ozge, Mark, Mark is of course completely right regarding the MPI error.., you're messing up something. Where was my mind? Sharp peaks in the RMSD and radius of gyration plots may indicate jumps over the periodic boundaries. But, that should not be a cause for breaking a simulation. The only parameter you mentioned that could be linked to the stability of the simulation is the nstcomm, the others only control output. Of course you should try to understand what made your simulation crash, in stead of treating symptoms, possibly covering up some flaw in the set up of the simulation. Check the .log file. Tsjerk On 3/29/07, Mark Abraham [EMAIL PROTECTED] wrote: ? wrote: Hi everybody, I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error : Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 7 additional processes aborted (not shown) This is just a generic MPI error message. You haven't established what has caused it yet. Try running the system for a short time on a single processor, to eliminate parallelism as a source of the problems (you'll need to re-grompp, of course). I only can think about the difference may be caused because of my protein -ligand complex is very big.It has 2 chains. After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy, nstxtcoutvalues than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics. Probably your topology is broken or your structure is insufficiently minimized or equilibrated. Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files? We can't tell yet, since you haven't told us any symptoms that are useful diagnostically. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genion halted
Dear list, the genion program gets halted when I'm trying to replace the solvent molecules with ions. The command genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top -pname NA+ -nname CL- -random -neutral -conc 0.1 asks for the group of solvent molecules and when I tell him to use it I get this output Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 9918 Processing topology Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ and 21 CL- ions. Back Off! I just backed up fdt.top to ./#fdt.top.2# Replacing solvent molecule 1163 (atom 6250) with NA+ and then nothing happens. genion.log gets generated only half way. My system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via synaptic and also built from source. The same thing happens in both of them. Gromacs version is 3.3.1. However, when I try the same thing on another machine, a HP Proliant ML350 with Debian Sarge and Gromacs 3.3.1, everything goes well. None of the gromacs programs gives any errors before genion. I'll give you more info about the system configuration if anyone asks :) Sampo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion halted
Hi, the same one, gcc-4.1. Have you tried with other versions? Sampo andrea spitaleri wrote: Hi which gcc have you used for compiling gromacs? I have the same problem in one pc in which I have build gromacs using gcc-4.1 Regards andrea Sampo Karkola wrote: Dear list, the genion program gets halted when I'm trying to replace the solvent molecules with ions. The command genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top -pname NA+ -nname CL- -random -neutral -conc 0.1 asks for the group of solvent molecules and when I tell him to use it I get this output Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 9918 Processing topology Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ and 21 CL- ions. Back Off! I just backed up fdt.top to ./#fdt.top.2# Replacing solvent molecule 1163 (atom 6250) with NA+ and then nothing happens. genion.log gets generated only half way. My system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via synaptic and also built from source. The same thing happens in both of them. Gromacs version is 3.3.1. However, when I try the same thing on another machine, a HP Proliant ML350 with Debian Sarge and Gromacs 3.3.1, everything goes well. None of the gromacs programs gives any errors before genion. I'll give you more info about the system configuration if anyone asks :) Sampo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion halted
Hi, so you got genion working with 4.0.2? Sampo andrea spitaleri wrote: gcc-4.0.2 seems ok for gmx-3.3.1 I have also submitted in bugzilla a similar problem with g_rdf Regards andrea Sampo Karkola wrote: Hi, the same one, gcc-4.1. Have you tried with other versions? Sampo andrea spitaleri wrote: Hi which gcc have you used for compiling gromacs? I have the same problem in one pc in which I have build gromacs using gcc-4.1 Regards andrea Sampo Karkola wrote: Dear list, the genion program gets halted when I'm trying to replace the solvent molecules with ions. The command genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top -pname NA+ -nname CL- -random -neutral -conc 0.1 asks for the group of solvent molecules and when I tell him to use it I get this output Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 9918 Processing topology Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ and 21 CL- ions. Back Off! I just backed up fdt.top to ./#fdt.top.2# Replacing solvent molecule 1163 (atom 6250) with NA+ and then nothing happens. genion.log gets generated only half way. My system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via synaptic and also built from source. The same thing happens in both of them. Gromacs version is 3.3.1. However, when I try the same thing on another machine, a HP Proliant ML350 with Debian Sarge and Gromacs 3.3.1, everything goes well. None of the gromacs programs gives any errors before genion. I'll give you more info about the system configuration if anyone asks :) Sampo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf again
Hi, I am using g_sdf to calculating the spatial distribution of lipid headgroups around other species in my system. The thing is when I get the gro file (produced by using the -r flag in g_sdf) and then look at this in vmd or chimera with my spatial density file (plt), the reference gro file is not positioned 'in' the box of density produced by g_sdf. Is this as it should be and I am interpreting my results incorrectly, or have I set up my coordinate system incorrectly? Many thanks in advance for help with this. -Syma *** Dr Syma Khalid Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K. *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Carbon Nanotube Simulations
Do you want to simulate an infinite nanotube or a finite one? Bob On 3/28/07, George Abadir [EMAIL PROTECTED] wrote: There is no C1 and C2 atom in the input PDB file, and the topology file is not generated because x2top doesn't generate a topology because of the errors. I don't understand what C (1) and C (2) means but it is not C1 and C2; I mean not two different types of atoms. The PDB file is generated simply from tubegen and I defined the residue type in the rtp file. Thanks Mark Abraham wrote: George Abadir wrote: Hi, thank you very much for your help. I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms at the ends of the tube into hydrogen atoms), but now I get an error No forcefield type for atom C(1) with 2 bonds instead of No forcefield type for atom C(2) with 1 bonds ! Is there any way to solve this? Not without knowing what's wrong with the topology for C1 and C2. That's your job :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
fulya caglar wrote: Hi Tsjerk, Thanks for your help.You're right about taking paths well walked by others,before starting new trails but I have to do this simulation for my study:( Then do it in a right way. Hurry up! Thanks very much for your suggestions again. Sincerely Fulya */Tsjerk Wassenaar [EMAIL PROTECTED]/* wrote: Hi Fulya, In addition to Mark's comments, if you have a friend who has the proper background for such parameterization he/she will know what to do and I don't need to describe the process. The basic thing is that if you're a novice with MD, it's best to first take the paths well walked by others, before starting new trails (in terms of methodology/parameters; I don't want to suggest to repeat projects from others, that's basically what tutorials are for, but I would advice to use proteins/dna with no strings attached). Regarding the mail server, the first two mails only arrived as forwarded mails, with a lot of junk around the main question (which makes reading less convenient). Best, Tsjerk On 3/28/07, Mark Abraham wrote: fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which varies considerably depending on the force field you're trying to extend. You should start by reading the paper that describes the parameterization of the force field you're trying to extend, and then thinking hard about how you can follow a similar process to get parameters that are consistent. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php We won't tell. Get more on shows you hate to love http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 (and love to hate): Yahoo! TV's Guilty Pleasures list. http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about making a pdb file
Hi all, I am a gromacs beginner. I am dealing with a 10-residue molecule each of which is un-natural amino acid called beta-peptide. I was wondering whether there is any option of making a PDB file so that I can use it to prepare the corresponding .gro file in gromacs. I somehow could generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac- version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Carbon Nanotube Simulations
A finite one. Thanks alot, George Robert Johnson wrote: Do you want to simulate an infinite nanotube or a finite one? Bob On 3/28/07, George Abadir [EMAIL PROTECTED] wrote: There is no C1 and C2 atom in the input PDB file, and the topology file is not generated because x2top doesn't generate a topology because of the errors. I don't understand what C (1) and C (2) means but it is not C1 and C2; I mean not two different types of atoms. The PDB file is generated simply from tubegen and I defined the residue type in the rtp file. Thanks Mark Abraham wrote: George Abadir wrote: Hi, thank you very much for your help. I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms at the ends of the tube into hydrogen atoms), but now I get an error No forcefield type for atom C(1) with 2 bonds instead of No forcefield type for atom C(2) with 1 bonds ! Is there any way to solve this? Not without knowing what's wrong with the topology for C1 and C2. That's your job :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] two chains
Hi Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain?Are the parameters must be different ?Also I want to ask about trajconv.Where I had to add the pbc?I want to send you my directions. 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr or is the pbc used in the script? Thank You very much Özge - It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about making a pdb file
Hi, Thanks, But is it possible to get the corresponding PDB format of that molcule from pymol after drawing it? Basically, I installed the pymol. But I could not find an option for writing the corresponding PDB structure of the entire molecule Jagannath On Mar 29, 2007, at 2:07 PM, Jay Mashl wrote: PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal wrote: Date: Wed, 28 Mar 2007 23:54:27 -0500 From: Jagannath Mondal [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] query about making a pdb file Hi all, I am a gromacs beginner. I am dealing with a 10-residue molecule each of which is un-natural amino acid called beta-peptide. I was wondering whether there is any option of making a PDB file so that I can use it to prepare the corresponding .gro file in gromacs. I somehow could generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac-version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf again
Syma, I am using g_sdf to calculating the spatial distribution of lipid headgroups around other species in my system. The thing is when I get the gro file (produced by using the -r flag in g_sdf) and then look at this in vmd or chimera with my spatial density file (plt), the reference gro file is not positioned 'in' the box of density produced by g_sdf. Is this as it should be and I am interpreting my results incorrectly, or have I set up my coordinate system incorrectly? That does sound a bit unusual. However, I use g_sdf quite extensively but don't use the reference structure function. Reason for this, is I have found that the one generated for the molecules I simulate it is highly distorted and the corresponding atom locations do not match up with where they they are located if you calculate the sdf for the non-coordinate atoms within the molecule. So I use a representative molecule, rotate to match the sdf for atoms within the molecule, then use that. Not the best way to do it, but it gets what I need. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about making a pdb file
See 'help save'. Apparently there is no menu option for saving the 'all' group. Jay On Thu, 29 Mar 2007, Jagannath Mondal wrote: Date: Thu, 29 Mar 2007 16:41:35 -0500 From: Jagannath Mondal [EMAIL PROTECTED] To: Jay Mashl [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] query about making a pdb file Hi, Thanks, But is it possible to get the corresponding PDB format of that molcule from pymol after drawing it? Basically, I installed the pymol. But I could not find an option for writing the corresponding PDB structure of the entire molecule Jagannath On Mar 29, 2007, at 2:07 PM, Jay Mashl wrote: PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal wrote: Date: Wed, 28 Mar 2007 23:54:27 -0500 From: Jagannath Mondal [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] query about making a pdb file Hi all, I am a gromacs beginner. I am dealing with a 10-residue molecule each of which is un-natural amino acid called beta-peptide. I was wondering whether there is any option of making a PDB file so that I can use it to prepare the corresponding .gro file in gromacs. I somehow could generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac-version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] two chains
? wrote: Hi You've asked four different questions in the space of one paragraph, with little clarity. Please consider asking each question with some organised background information that you think will help us give you the answer you want. Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain? No. If there's a covalent link then they'll need to end up as one molecule, otherwise more than one. Are the parameters must be different ? No. Why would they? Also I want to ask about trajconv. What did you want to ask? :-) Where I had to add the pbc?I want to send you my directions. As Dallas said, you introduce pbc with your choice of parameters in your .mdp file. It sounds like you should learn some things by looking at your .mdp files and understanding the effects of each parameter by looking them up in section 7.3 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr or is the pbc used in the script? What script? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] two chains
özge kül wrote: Hi Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain? Yes. There is difference. But somehow, you need to rephrase your question. Are the parameters must be different ?Also I want to ask about trajconv.Where I had to add the pbc? the second step, editconf impose PBC onto the system. I want to send you my directions. 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr or is the pbc used in the script? Thank You very much Özge It's here! Your new message! Get new email alerts http://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/ with the free Yahoo! Toolbar. http://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Orientation of DMSO
Dinesh Pinisetty wrote: Hello, As suggested I tried using g_order with an .ndx file for only DMSO molecules. I did get an output file which did not have anything in it. # This file was created by g_order which is part of G R O M A C S: # GROningen MAchine for Chemical Simulation # All this happened at: Thu Mar 29 17:00:05 2007# @ title Order tensor diagonal elements @ xaxis label Atom @ yaxis label S @TYPE xy I did not get any data, what I desire to achieve is to get an orientation profile for DMSO molecules. Can anyone please suggest me how to achieve it. Sincerely, Dinesh. I didn't follow this thread, but g_order is not what you want. You may want to try g_dipoles -sl instead. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
