[gmx-users] block averaging in g_energy vs. g_analyze
Dear gurus, I'm trying to calculate some statistics for the coulomb-sr and coulomb-recip energies in my system (200 ns simulation). I Suppose the underlying algorithms in g_energy and g_analyze for making the error estimate are pretty much the same, but in g_energy the sampling is more accurate which can cause some differences. However, I'm confused about two points 1. What can be the cause of nan as g_energy output rmsd when the mean is ok (and also g_analyze gives ok rmsd)? 2. g_analyze gives me an error regarding set 1. I think this error implies not-long-enough sampling (longer correlation than run time), but can there be another cause for this? In this case the correlation would be very, very long. I have enclosed the output from g_energy and g_analyze. All help will be appreciated! Yours, Hanne g_energy: the last energy frame read 10002 time 20.000 Statistics over 99984548 steps [ 0. through 20. ps ], 2 data sets All statistics are over 1686 points Energy Average Err.Est. RMSD Tot-Drift --- Coulomb (SR) -1.98611e+06 27nan133.058 (kJ/mol) Coul. recip.-470752 5.7nan -18.7256 (kJ/mol) g_analyze: Read 2 sets of 10003 points, dt = 19.996 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 -1.986081e+06 2.158308e+03 2.158093e+01 0.0030.006 SS2 -4.707511e+05 9.907673e+01 9.906682e-01 0.0050.014 a fitted parameter is negative invalid fit: e.e. 22.6293 a 1.04171 tau1 14.54 tau2 99.5578 Will fix tau2 at the total time: 20 Set 1: err.est. 76.0536 a 0.999443 tau1 12.7992 tau2 20 Set 2: err.est. 6.73835 a 0.926159 tau1 13.7527 tau2 6092.31 gcq#135: Check Your Input (D. Van Der Spoel) -- 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 append the run
Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. What should be the problem.I need to append my run. -- Regards N.NagaSundaram -- 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] xmgrace graphs
On 10/3/12 12:06 AM, naga sundar wrote: Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. Distance plots produced by g_dist have four data sets (distance and x,y,z components) so plotting in this way can be quite messy. Leave out the -nxy if you want to only plot the total distance and not the remaining (x,y,z) components. -Justin On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Density measurment
On 10/3/12 12:22 AM, rama david wrote: Thank you Justin for your reply , I tried g_density again after your reply. But I found that it give density with respect to box dimension and not to time. I suggested before that you could perhaps advantageously using the -b and -e flags to achieve something similar. You cannot get density over time per region of the box automatically. That would be some sort of 3-D graph since there are two quantities effectively being analyzed. g_densmap have xpm output and no the xvg ( I need density or no of water molecule present in between two peptides with respect to the time ).. The colorized plot from g_densmap can tell you quite a lot, in my opinion. What about g_rdf? Integrating an RDF plot will tell you how many solute molecules are present in a particular region of space. Otherwise, you can also use g_select to determine how many water molecules are located between your peptides using simple geometric criteria. Look for examples in the archive; people have done this before. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding append the run
On 10/3/12 6:10 AM, naga sundar wrote: Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. -cp is not a valid option. What you want is -cpi in your command line. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tyrosyl radical force field
On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechanics force fields do not deal explicitly with electrons, so don't expect anything particularly interesting to happen with a so-called radical tyrosine unless you're using QM methods. You could perhaps parameterize a deprotonated tyrosine residue that, as input to QM software, has the number of electrons in the radical species. You may then have to come up with new atom types depending upon whether or not the LJ parameters (especially for the phenolic O) are satisfactory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
On 10/3/12 1:59 AM, James Starlight wrote: Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? genbox decides whether or not to put molecules in the box if they can be added intact; anything sticking out of the box is removed. Since water molecules are small, this is easy to do. Since a lipid molecule is large, it is not so easy. The hydrocarbon tails are very flexible and thus may have configurations leading them to stick out of the box, so genbox won't add them. You will likely have to gradually increase the box dimensions in x and y to allow for more lipids to be added, striking a balance between the (much larger) number of water molecules and number of lipids added. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: The largest charge group contains 1000 atoms
On 10/3/12 1:40 AM, Ashok Kumar Das wrote: Dear Dr. Justin A. Lemkul, I am Dr. Ashok Kumar Das from IHPC, Singapore. I am a new GROMACS learner. The system I wish to simulate contains 125 polymer chains, each chain containing 8 beads (CH3 and CH2 groups). These beads do not have any charge on them. I mention charge = 0.0 in the *.gro file. There are no charges in .gro files. If you have manipulated the .gro file by adding new information, you will break its format. In the *.gro file, the chains are arranged sequentially, making a total of 1000 atoms. I use atom names as 'CH3' and 'CH2', with zero charge. However, on running 'grompp' to make the *.tpr file, I get the error message: The largest charge group contains 1000 atoms. The maximum is 32. Kindly guide us how to correct the problem. I think the error message speaks for itself. You have every atom of your system in a single charge group. You don't have any charges on the atoms, but the size of the charge group will have negative implications for neighbor searching. Consult the manual about what a charge group is and how it is used. Normal charge groups are between 1-4 atoms in size, depending on the nature of the group. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding append the run
Thanks justin got it... On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:10 AM, naga sundar wrote: Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. -cp is not a valid option. What you want is -cpi in your command line. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- 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] tyrosyl radical force field
Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechanics force fields do not deal explicitly with electrons, so don't expect anything particularly interesting to happen with a so-called radical tyrosine unless you're using QM methods. You could perhaps parameterize a deprotonated tyrosine residue that, as input to QM software, has the number of electrons in the radical species. You may then have to come up with new atom types depending upon whether or not the LJ parameters (especially for the phenolic O) are satisfactory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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] tyrosyl radical force field
On 10/3/12 7:49 AM, tarak karmakar wrote: Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? That doesn't sound legitimate to me at all. A radical species is electronically very different. -Justin On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechanics force fields do not deal explicitly with electrons, so don't expect anything particularly interesting to happen with a so-called radical tyrosine unless you're using QM methods. You could perhaps parameterize a deprotonated tyrosine residue that, as input to QM software, has the number of electrons in the radical species. You may then have to come up with new atom types depending upon whether or not the LJ parameters (especially for the phenolic O) are satisfactory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tyrosyl radical force field
It's a radical approach, for certain! But do mind that the tyrosyl side chain is a conjugated system, so the charge goes all over the place, and you have to do (proper) QM calculations to see where it ends up. Radical approaches are not suitable for radical parameters :p Tsjerk On Wed, Oct 3, 2012 at 2:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 7:49 AM, tarak karmakar wrote: Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? That doesn't sound legitimate to me at all. A radical species is electronically very different. -Justin On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechanics force fields do not deal explicitly with electrons, so don't expect anything particularly interesting to happen with a so-called radical tyrosine unless you're using QM methods. You could perhaps parameterize a deprotonated tyrosine residue that, as input to QM software, has the number of electrons in the radical species. You may then have to come up with new atom types depending upon whether or not the LJ parameters (especially for the phenolic O) are satisfactory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Coordinate file for lipid bilayer
Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 1:59 AM, James Starlight wrote: Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? genbox decides whether or not to put molecules in the box if they can be added intact; anything sticking out of the box is removed. Since water molecules are small, this is easy to do. Since a lipid molecule is large, it is not so easy. The hydrocarbon tails are very flexible and thus may have configurations leading them to stick out of the box, so genbox won't add them. You will likely have to gradually increase the box dimensions in x and y to allow for more lipids to be added, striking a balance between the (much larger) number of water molecules and number of lipids added. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Coordinate file for lipid bilayer
On 10/3/12 8:59 AM, James Starlight wrote: Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png I don't know if that will have much of an effect or not. The values in vdwradii.dat are used to determine if there is atomic overlap with coordinates being added (solvent) to the solute configuration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tyrosyl radical force field
Thanks Tsjerk, In my system, I need to model one of the TYR side chains in radical form. Now while doing that I need to get proper charges as you said. According I have calculated the ESP charges in Gaussian for the TYR radical [ unprotonated,neutral, terminals are capped with -NMe and -COCH3] . Now can I take these charges to simulate the entire protein? Can you please suggest me a proper protocol and some ways to get proper charges (RESP e'm trying) to deal with this problem? Thanks On Wed, Oct 3, 2012 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: It's a radical approach, for certain! But do mind that the tyrosyl side chain is a conjugated system, so the charge goes all over the place, and you have to do (proper) QM calculations to see where it ends up. Radical approaches are not suitable for radical parameters :p Tsjerk On Wed, Oct 3, 2012 at 2:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 7:49 AM, tarak karmakar wrote: Thanks Justin, Actually if I would remove the proton from the tyrosine -OH and add the corresponding charge of the Hydrogen to the phenolic oxygen to keep the residue neutral then wouldn't it be convenient to think as if it's a radical ? That doesn't sound legitimate to me at all. A radical species is electronically very different. -Justin On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:00 AM, tarak karmakar wrote: Dear All, Is it possible to deal a protein with tyrosyl radical in Molecular Dynamics Simulation ?? If possible can you please provide me the reference or literature where I can find the force field parameters for tyrosyl radical ? Molecular mechanics force fields do not deal explicitly with electrons, so don't expect anything particularly interesting to happen with a so-called radical tyrosine unless you're using QM methods. You could perhaps parameterize a deprotonated tyrosine residue that, as input to QM software, has the number of electrons in the radical species. You may then have to come up with new atom types depending upon whether or not the LJ parameters (especially for the phenolic O) are satisfactory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 -- Tarak -- 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] Temperature in simulation
Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. Thanks in advance for your suggestions. Sincerely, Shima -- 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] Temperature in simulation
You should do NVT equilibration to your target temperature. Your system is already heavily changed between the equilibrated full bilayer and the embedded protein system so velocities will be reassigned anyway. On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. Thanks in advance for your suggestions. Sincerely, Shima -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Temperature in simulation
On 10/3/12 9:39 AM, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? Well, what is the goal of your simulation? If you're trying to simulate a physiological environment (human body/cells) then 310 K is the correct temperature. If you're trying to replicate some other in vitro conditions, that should motivate your choice. As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. A 10 K increase shouldn't affect the protein dynamics all that strongly. What problems have you seen, and why do you expect them to carry over to a membrane environment? One of the most important factors in choosing the temperature of a lipid bilayer is the phase transition temperature of the lipids. POPC should be fluid at either 300 K or 310 K, so that is not a concern. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature in simulation
I see that the velocities will be reassigned, but what I'm concerned about, is reporting the results in a paper. How would it be? Thanks for your suggestion Peter. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:16 PM Subject: Re: [gmx-users] Temperature in simulation You should do NVT equilibration to your target temperature. Your system is already heavily changed between the equilibrated full bilayer and the embedded protein system so velocities will be reassigned anyway. On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. Thanks in advance for your suggestions. Sincerely, Shima -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Temperature in simulation
On 10/3/12 9:57 AM, Shima Arasteh wrote: I see that the velocities will be reassigned, but what I'm concerned about, is reporting the results in a paper. How would it be? That all depends on the answers to my previous questions, as well as the following: why did you simulate the protein in water prior to its insertion in a membrane? There may be logical reasons to do this, but if it's a membrane protein and thus largely hydrophobic (I'm assuming), then why simulate it in water where it is likely to be unstable? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. Thank you Elie . Date: Tue, 2 Oct 2012 03:56:28 + . From: emanuel.bi...@monash.edu . Subject: RE: [gmx-users] Error with grompp To: gmx-users@gromacs.org Hi Elie, Your email is a bit confusing but I will try to give you some idea as per my understanding of your email. If you want to use top and itp files separately, you should put all the info (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you should use # include your itp file.itp in your top file. No atom, bond, pair etc in your top file. Just like you include your water type (spc/tip4) you should include the itp. And top of that you should put the right number of molecules in the right order in your top file at the (molecules) section. Hope that might give you some help. Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Elie M Sent: Tuesday, 2 October 2012 1:39 PM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Error with grompp I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it
Re: [gmx-users] Temperature in simulation
It sounds like you want to report that you created a bilayer, equilibrated it at 310K then inserted the protein and ran MD of the embedded system at 300K? On 2012-10-03 06:57:22AM -0700, Shima Arasteh wrote: I see that the velocities will be reassigned, but what I'm concerned about, is reporting the results in a paper. How would it be? Thanks for your suggestion Peter. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:16 PM Subject: Re: [gmx-users] Temperature in simulation You should do NVT equilibration to your target temperature. Your system is already heavily changed between the equilibrated full bilayer and the embedded protein system so velocities will be reassigned anyway. On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. Thanks in advance for your suggestions. Sincerely, Shima -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Error with grompp
On 10/3/12 10:03 AM, Elie M wrote: Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: That doesn't really make any sense. You've chopped out the information for your molecule from the topology that g_x2top wrote, then simply re-included that information? The output of g_x2top should be a functional topology; you should not have to adjust it. If you need this topology to be an .itp file, i.e. as a ligand in some other .top, then you only need to make small adjustments. See the following: http://www.gromacs.org/Documentation/File_Formats/.itp_File ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 I don't know whether it is your email client or the topology itself, but the seemingly random line breaks make these posts very difficult to read. [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. A topology follows a defined structure that must be observed. The hierarchy is described in the manual, but can be distilled into the following requirements: 1. You must #include a force field that defines all default elements (i.e. a [defaults] directive) that govern how the force field operates. 2. You must #include the nonbonded and bonded parameters for that force field, in that order. Bonded parameters are assigned based on atom types, which must be declared first in order to be used. 3. After all force field-level parameters (items 1 and 2), you can introduce molecules that use these parameters. This is the point where you can proceed to [atoms], [bonds], etc for a particular molecule. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature in simulation
Actually, I want to study this system of protein-membrane, trying to replicate in vitro conditions and then studying function of the protein. I simulated the protein in water to see the usual result : losing its native configuration. Then, I am trying to insert the protein in membrane to study its function. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:18 PM Subject: Re: [gmx-users] Temperature in simulation On 10/3/12 9:39 AM, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? Well, what is the goal of your simulation? If you're trying to simulate a physiological environment (human body/cells) then 310 K is the correct temperature. If you're trying to replicate some other in vitro conditions, that should motivate your choice. As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. A 10 K increase shouldn't affect the protein dynamics all that strongly. What problems have you seen, and why do you expect them to carry over to a membrane environment? One of the most important factors in choosing the temperature of a lipid bilayer is the phase transition temperature of the lipids. POPC should be fluid at either 300 K or 310 K, so that is not a concern. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature in simulation
yes, that's right. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:37 PM Subject: Re: [gmx-users] Temperature in simulation It sounds like you want to report that you created a bilayer, equilibrated it at 310K then inserted the protein and ran MD of the embedded system at 300K? On 2012-10-03 06:57:22AM -0700, Shima Arasteh wrote: I see that the velocities will be reassigned, but what I'm concerned about, is reporting the results in a paper. How would it be? Thanks for your suggestion Peter. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 5:16 PM Subject: Re: [gmx-users] Temperature in simulation You should do NVT equilibration to your target temperature. Your system is already heavily changed between the equilibrated full bilayer and the embedded protein system so velocities will be reassigned anyway. On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote: Hi all, I want to insert a protein in POPC lipid bilayer. First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be incorrect logically ? As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer. Thanks in advance for your suggestions. Sincerely, Shima -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Coordinate file for lipid bilayer
Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 8:59 AM, James Starlight wrote: Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png I don't know if that will have much of an effect or not. The values in vdwradii.dat are used to determine if there is atomic overlap with coordinates being added (solvent) to the solute configuration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Coordinate file for lipid bilayer
On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature in simulation
On 10/3/12 10:16 AM, Shima Arasteh wrote: Actually, I want to study this system of protein-membrane, trying to replicate in vitro conditions and then studying function of the protein. I simulated the protein in water to see the usual result : losing its native configuration. Then, I am trying to insert the protein in membrane to study its function. Inserting an unfolded (or partially unfolded) protein into a membrane and hoping it reflects reality may or may not be wise. If you want to compare water vs. membrane environments, those should be two separate simulations, both starting from the same (presumably) native state of the protein. If you're hoping that the protein will re-fold within the membrane, you're probably making a large number of assumptions, most of which may not hold up under scrutiny. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature in simulation
You are right and I will insert the native protein in membrane. To do so, I want to set the temperature of nvt.mdp file to 300 K, however I want to use the result output of memrane simulated in 310 K for 50 ns. Through your earlier suggestions, I got that velocities would be reassigned in new simulation and 10 degree is not a thing to be concerned in my system. Here, I'd like to know if I am criticized for using this difference between temperatures? Thanks for all your suggestions, that are all kind of you :-) Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, October 3, 2012 8:44 PM Subject: Re: [gmx-users] Temperature in simulation On 10/3/12 10:16 AM, Shima Arasteh wrote: Actually, I want to study this system of protein-membrane, trying to replicate in vitro conditions and then studying function of the protein. I simulated the protein in water to see the usual result : losing its native configuration. Then, I am trying to insert the protein in membrane to study its function. Inserting an unfolded (or partially unfolded) protein into a membrane and hoping it reflects reality may or may not be wise. If you want to compare water vs. membrane environments, those should be two separate simulations, both starting from the same (presumably) native state of the protein. If you're hoping that the protein will re-fold within the membrane, you're probably making a large number of assumptions, most of which may not hold up under scrutiny. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Temperature in simulation
On 10/3/12 2:02 PM, Shima Arasteh wrote: You are right and I will insert the native protein in membrane. To do so, I want to set the temperature of nvt.mdp file to 300 K, however I want to use the result output of memrane simulated in 310 K for 50 ns. Through your earlier suggestions, I got that velocities would be reassigned in new simulation and 10 degree is not a thing to be concerned in my system. Here, I'd like to know if I am criticized for using this difference between temperatures? It would be preferable to equilibrate the membrane at the desired temperature before perturbing it with the introduction of a protein. I would assume that any effect on the dynamics would be minimal, but assumptions don't get you past a critical audience. It can't hurt to run a short equilibration (10-20 ns maybe) of the membrane at 300 K before introducing the peptide. It's more intuitive and should not take very long to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Gromacs users, I would like to simulate water on Ruthenium surface. Would you please suggest the force field used to describe Ru. Many 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
Re: [gmx-users] (no subject)
On 10/3/12 5:17 PM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate water on Ruthenium surface. Would you please suggest the force field used to describe Ru. You're not likely to find one built into Gromacs by default. http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum Elie Date: Wed, 3 Oct 2012 10:15:07 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/3/12 10:03 AM, Elie M wrote: Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: That doesn't really make any sense. You've chopped out the information for your molecule from the topology that g_x2top wrote, then simply re-included that information? The output of g_x2top should be a functional topology; you should not have to adjust it. If you need this topology to be an .itp file, i.e. as a ligand in some other .top, then you only need to make small adjustments. See the following: http://www.gromacs.org/Documentation/File_Formats/.itp_File ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 I don't know whether it is your email client or the topology itself, but the seemingly random line breaks make these posts very difficult to read. [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. A topology follows a defined structure that must be observed. The hierarchy is described in the manual, but can be distilled into the following requirements: 1. You must #include a force field that defines all default elements (i.e. a
Re: [gmx-users] xmgrace graphs
Thanks On Wed, Oct 3, 2012 at 6:04 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 12:06 AM, naga sundar wrote: Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. Distance plots produced by g_dist have four data sets (distance and x,y,z components) so plotting in this way can be quite messy. Leave out the -nxy if you want to only plot the total distance and not the remaining (x,y,z) components. -Justin On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Error with grompp
On 10/3/12 7:48 PM, Elie M wrote: Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum It seems like the format of whatever files you're using is horribly broken. I would recommend starting over and not making any adjustments to any files (removing lines, changing contents, adding comments, etc) unless you know exactly what you're doing. For example, the presence of '\par' in ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text editor). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atomtype F not found
On 10/3/12 10:43 PM, Nur Syafiqah Abdul Ghani wrote: Dear Users, Right now i already done for creating the a gro file from antechamber to gromacs format of my molecule which is hexafluoroisopropanol. But when i want to minimize it in vacuum it show atomtype F not found. Im using oplsaa force field and i already change the atom type according to the force field. Below are my files that i need to used for my minimization : PDB file : HETATM1 opls_164 HFI A 101 -1.433 -1.291 -0.584 1.00 -0.219790 HETATM2 opls_161 HFI A 101 -1.274 -0.111 -0.039 1.00 0.600750 HETATM3 opls_164 HFI A 101 -1.331 -0.244 1.257 1.00 -0.208510 HETATM4 opls_164 HFI A 101 -2.292 0.639 -0.413 1.00 -0.235630 HETATM5 opls_158 HFI A 101 0.013 0.562 -0.520 1.00 0.064010 HETATM6 opls_078 HFI A 101 0.068 1.864 -0.080 1.00 -0.549590 HETATM7 opls_079 HFI A 101 -0.560 2.404 -0.527 1.00 0.438940 HETATM8 opls_140 HFI A 101 0.014 0.485 -1.602 1.00 0.103910 HETATM9 opls_161 HFI A 101 1.289 -0.122 -0.036 1.00 0.652070 HETATM 10 opls_164 HFI A 101 2.323 0.430 -0.620 1.00 -0.216720 HETATM 11 opls_164 HFI A 101 1.282 -1.395 -0.353 1.00 -0.223970 HETATM 12 opls_164 HFI A 101 1.450 -0.022 1.254 1.00 -0.205480 CONECT12 CONECT21345 CONECT32 CONECT42 CONECT52678 CONECT65 CONECT75 CONECT859 10 11 CONECT98 CONECT 108 CONECT 118 12 CONECT 12 11 END also the topology ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include organic solvent #include hfi.itp ; Include water topology #include oplsaa.ff/spc.itp #ifdef POSRER_WATER ; Position restraint for each water oxygen [position_restraints] ; i funct fcx fcy fcz 11 1000 1000 1000 #endif [system] ;Name solute [molecules] ;Compound #mols HFI 1 gro file; solvent_HFI.gro.gro created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005 12 1HFI opls_1641 0.354 0.142 0.000 1HFI opls_1612 0.369 0.260 0.055 1HFI opls_1643 0.364 0.247 0.184 1HFI opls_1644 0.267 0.335 0.017 1HFI opls_1585 0.498 0.328 0.006 1HFI opls_0786 0.503 0.458 0.050 1HFI opls_0797 0.440 0.512 0.006 1HFI opls_1408 0.498 0.320 -0.102 1HFI opls_1619 0.626 0.260 0.055 1HFI opls_164 10 0.729 0.315 -0.004 1HFI opls_164 11 0.625 0.132 0.023 1HFI opls_164 12 0.642 0.270 0.184 0.625250.132330.02309 is there something wrong of my file? Your .pdb and .gro files call opls_* atom names, which are actually atom types. Do not confuse the two. Why it cant recognize the F atom?? Without seeing the contents of hfi.itp, it's hard to say aside from the general statement that you're using an atom type that does not exist. I suspect you've confused atom types and names, given the coordinate files shown. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with the installation of Gromacs 4-5.5
Hi Deepak, Is the gromacs is in your path?? Please mention your operating system.. With best wishes and Regards, rama david On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote: Dear All I want to use Amber force field in Gromacs therefore I installed the latest version of Gromacs and installed accordingly as per as the instructions given in INSTALL.automake file. ./configure make make install It works fine and shows the message that installation is complete but none of the commands like pdb2gmx,mdrun works.Even the luck does not works which is meant to test the installation of gromacs. What is the issue with the installation.Please help me resolve it. Regards DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- 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
Re: [gmx-users] Coordinate file for lipid bilayer
Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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
