[gmx-users] Re: methanol simulation error
gd_4 29313334 1gd_19 31333436 1gd_20 33343638 1gd_4 34363842 1gd_19 36383940 1gd_17 36384244 1gd_20 38424445 1gd_4 42444549 1gd_19 45444847 1gd_19 44454647 1gd_17 44454951 1gd_20 45464748 1gd_17 46474844 1gd_17 45495153 1gd_4 49515354 1gd_19 51535456 1gd_20 53545658 1gd_4 54565862 1gd_19 56585960 1gd_17 56586264 1gd_20 58626466 1gd_4 62646667 1gd_19 64666769 1gd_20 [ dihedrals ] ; aiajakal functc0c1 c2c3 5 1 9 6 2gi_2 5 7 8 6 2gi_2 9 51110 2gi_1 11 91215 2gi_1 12111613 2gi_2 16121817 2gi_1 18162019 2gi_1 21202322 2gi_1 23212524 2gi_1 25232926 2gi_2 25272826 2gi_2 29253130 2gi_1 31293332 2gi_1 34333635 2gi_1 36343837 2gi_1 38364239 2gi_2 38404139 2gi_2 42384443 2gi_1 44424548 2gi_1 45444946 2gi_2 49455150 2gi_1 51495352 2gi_1 54535655 2gi_1 56545857 2gi_1 58566259 2gi_2 58606159 2gi_2 62586463 2gi_1 64626665 2gi_1 67666968 2gi_1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/methanol.itp [ system ] ; Name Protein in methanol [ molecules ] ; Compound#mols Protein 1 MTH 660 Message: 7 Date: Fri, 07 Jan 2011 12:41:27 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] methanol simulation error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d266f47.5000...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/01/2011 12:31 PM, mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include gromos43a1.ff/methanol.itp line to .top. I'm not sure why I'm repeating myself, but the name given in that moleculetype is not SOL. That name must match what appears in the [molecules] section. Please make sure you have read the examples in Chapter 5 of the manual and understand everything there. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? You're using atomtype CMET somewhere in your .top or its #included .itp files. Your forcefield doesn't define atomtype CMET, and it needs to if your usage is correct. Without seeing your topology, we can't say more. 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] Re: Re: methanol simulation error
Daer Justin, I changed the last line as MTH 660 I got the same error, Atomtype CMET not found Do you mean this? best wishes mustafa Message: 1 Date: Fri, 07 Jan 2011 07:04:05 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: methanol simulation error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d270135.5000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed mustafa bilsel wrote: snip ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/methanol.itp This topology defines the [moleculetype] name as Methanol, which is the name that needs to be used in the [molecules] directive below. But then, too, you're not using the same residue name either (MTH instead of MeOH), so it is still not possible to say what's going wrong. -Justin [ system ] ; Name Protein in methanol [ molecules ] ; Compound#mols Protein 1 MTH 660 -- == == Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] justin
Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. mustafa This topology defines the [moleculetype] name as Methanol, which is the name that needs to be used in the [molecules] directive below. But then, too, you're not using the same residue name either (MTH instead of MeOH), so it is still not possible to say what's going wrong. -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] methanol simulation
Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added anything like in water simulation -water tip3p. Should we add something to tell the gromacs that it is methanol simulation? best wishes mustafa -- 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] methanol simulation
Dear Mark, so, what should I do? mustafa -- 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] methanol simulation error
Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include gromos43a1.ff/methanol.itp line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- 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] CNT
Hi all, Could you tell me a program to obtain topol.top for a CNT? In CNT.pdb residues are efined as UNK. best wishes mustafa -- 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] minimization
Hi all, At the end of the minimisation I obtained potential energy value approximately -40,000 and I see the following warning Stepsize too small, or no change in energy.Converged to machine precision, but not to the requested precision Fmax 10 As far as I know for succesful minimisation potential energy must be between -100,000 and -1,000,000. My em.mdp file as follows integrator= steep emstep=0.1 nsteps=1000 nstlist=10 rlist=1.0 coulombtype=pme rcoulomb=1.0 vdw-type=cut-off rvdw=1.0 nstenergy=10 My minimisation stops at approximately 19,000 th step. Is my minimisation acceptable?If no, how can I correct it? best wishes Mustafa -- 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] minimization
Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did do_dssp I have the below error. Although the dssp exe is in /usr/local/bin and also I did export, computer couldn't find dssp exe file. What is the problem? What should I do? Best wishes Mustafa - Select a group: 5 Selected 5: 'MainChain' There are 90 residues in your selected group Reading frame 0 time0.000 Back Off! I just backed up ddt2Vei2 to ./#ddt2Vei2.1# --- Program do_dssp, VERSION 4.5.1 Source code file: do_dssp.c, line: 521 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddt2Vei2 ddPcoaqM /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Learn what your shell uses and apply it. You're more than likely running bash, in which case export is the command to use. -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] minimization
Hi, What is the meaning of the below message after I completed minimization? Does it mean minimization is successful? In my input parameters nsteps=10,000,000 but minimization stops at about 14,000 th step. Is 10,000,000 very large? What is the typical value for it? And also what is the meaning of Fmax10? Message: Converged to machine precision, but not to the requested precision Fmax10. Best wishes Mustafa -- 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 size continuing the previous energy minimization
Hi, 1. How can I learn the box shape and size of a completed simulation? 2. I want to keep going the previous completed energy minimization by increasing nsteps. How can I do this? Best wishes Mustafa -- 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] dssp problem
Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Best wishes -- 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] dssp
Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about 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] writing the means of every 100 potential energies into an output file
Hi, I want to write the means of every 100 potential energies into an output file. Is there an option in Gromacs to do this? Best wishes -- 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] What can we do with gromacs?
Hi, I would like to ask questions about what we can do with Gromacs. 3. For example I have some different molecules and I would like to see their binding affinity to carbon nanotubes. Is it possible to do this simulation with Gromacs? If possible, I should have attractive and repulsive potentials. Which potential(s) in Gromacs should I use for this purpose? 2. Is it possible to simulate folding mechanism of a protein in closed geometry? closed geometry maybe in cylindrical or cubic shape. 3. Can we check if a protein adhesed or not a to a surface? surface consists of atoms. Best wishes Mustafa Bilsel -- 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] elastin
Hi all, I would like to simulate (VPGVG)18, but it is pdb isn't in protein data bank. Where can I find it? OR How can I simulate it under this condition? Best wishes -- 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 shape
Dear Lina, could you express these commands clearly? I am a new user! editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_ box.gro -center x/2 y/2 z/2 -box x y z genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o they_are_in_the_same_box_now.gro -p topol.top -- 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] editconf
Hi, when I choose different box types and draw them by Pymol, I see no visual difference between them. At least cubic must be different from the others. What is the reason for this? best wishes -- 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
