[gmx-users] Enterobactin binding to Iron(III)
I was told before I would need to use quantum calculations to do this. What software and method would you suggest to do this? Thanks. -Jonathan Saboury -- 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] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)
Hello everybody, I am sorry to do this, but I only have knowledge in ochem (haven't taken pchem yet) so reading Car-Parrinello Molecular Dynamics and searching it on wikipedia yields no data that I understand. So what I'll do to save everyone time is to share what I want to do and ask if this software can do it, and if not, do you know of any software that can do this? My goal is to simulate Iron(III)Hydroxide in a box of water (perhaps physiological conditions/ions) with Enterobactin, to see if it will form an iron complex. Perhaps this is more for a quantum chemistry program? Any that you would suggest to use? Thank you for your time. -Jonathan Saboury -- 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] Iron(III) Chloride in water
I want to simulate Iron(III) Chloride in water (in order to test some iron sequestering agents). I've tried to use acpype to generate an iron ion but it errors. So I used genion and labelled the positive ion FE with charge of 3. However grompp does not recognize the atom FE. My question is how would I simulate this? Commands: http://pastebin.com/raw.php?i=0B3EW7mF Files: http://www.sendspace.com/file/rc8el9 Thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Deuterate organic solvent
I want to run a simulation of cyclohexane in deuterated chloroform. I was able to run a sim of cyclohexane in regular chloroform, but unable to find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh and -deuterate option, would I do it this way? It isn't a protein and would assume I would get an error. I know these sims are based off of newton's laws of motion, and that is pretty much where my understanding stops. I assume that the hydrogen’s have a mass of ~1, and that I need to change them to ~2. I look at the .itp's generated by acpype and all the masses are set to 0 (is this alright?) Note: all [atomtypes] are in cyclohexane_GMX.itp. Another problem I see happening that the atomtypes are all sharing the same atomtype, so possibly any sp3 C-H bond is going to be deuterated since they all share the same definition. commands: http://pastebin.com/raw.php?i=jGZV8k2t cyclohexane_GMX.itp: http://pastebin.com/raw.php?i=Q6MrURmN chloroform_GMX.itp: http://pastebin.com/raw.php?i=pAHaUSVv Entire folder download: http://www.sendspace.com/file/frc1uy Is there an automatic way to have a specific solvent be deuterated? Thank you for the help :)) -- 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] Funky output trajectory (lines all over the place)
I tried minimizing a box of cyclohexanes and water. The first frame is fine, but after that seemingly random lines form in vmd with the cyclohexanes. The waters seem to minimizing just fine though. I am sure I am just doing something extremely silly and I just don't know it because of ignorance. I have no formal training on simulations, you are my only hope! Perhaps using the em.gro with the em.trr is not the correct way to visualize? I used the command: vmd em.gro em.trr Or something is wrong with my em.mdp? em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj Here are all the files, in case you need them: http://www.sendspace.com/file/gx8j97 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading about the mdp file format but i only understand ~5%. If I could have done more I would have tried :/ Thank you all, it is really appreciated. -Jonathan Saboury -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 113, Issue 101
That said, there is an spc.itp within the AMBER subdirectories that needs to be #included more explicitly, i.e. #include amber99sb.ff/spc.itp May I ask why you are using SPC? The AMBER force fields were parametrized with TIP3P, so I see no viable reason to use a different water model. Ah, fixed and works like a charm, thank you :) To be completely honest I was using it out of ignorance. I've just been checking what has worked for me in tutorials and been working from there to something I am more interested in. It's not a bug, because genbox does not advertise such a feature. genbox is hard-coded to only ever deal with water. Anything else is up to the user. Interesting, any reason a user would not want such a feature? Any force field can be parametrized to give correct target data, especially for a molecule as simple as cyclohexane. What I use is a complex question, because it depends entirely upon the task at hand :) Can you list a few so I can go check them out on my own? It would be appreciated :) Thank you Justin, I appreciate your time you give helping me :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: No such moleculetype SOL
Then something is wrong with the way you've done it, because the job of spc.itp is to define the [moleculetype] SOL and all its relevant parameters. Hm...not sure what the matter is. Added a forcefield as well as spc.itp to the .top file made by acpype. Still getting the error Fatal error: No such moleculetype SOL Here is a list of commands and explanations of what I did: http://pastebin.com/raw.php?i=V5wrRdme Here is the .top: http://pastebin.com/raw.php?i=LzCANQZw Here are the files I am using: http://www.sendspace.com/file/5ps0i1 It is important to note that genbox did not add the amount of cyclohexanes added to system in the .top (it did do it for the waters though). Perhaps that is a bug? You need a parent force field that defines all the bonded and nonbonded interactions in the system. Whether or not this is one that comes with Gromacs or one you design yourself, you still have to satisfy all of the internal mechanics (see Chapter 5). Whether or not there is a protein is completely irrelevant; force fields do much more than just proteins. I see, interesting. Added it to the .top :) Well, PRODRG parameters are pretty low-quality anyway, but it's a convenient example for doing a tutorial rather than trying to teach people how to use other external software ;) As you know I am using acpype, is it any better? What do you use? Thank you for the help Justin, it is extremely appreciated :) -- 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 such moleculetype SOL
I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- 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: No such moleculetype SOL
Have a look at how Justin's tutorial's .top gets access to a water topology. Mark Thank you very much for the response Mark! I've looked at his .top and it seems to me that how he included it is by adding #include spc.itp. I've added that line to cyclohexane.top before and after the #include cyclohexane.itp with no success (same error as before). I also saw that he added a force field. Would I need to do this if I am not interested in a protein? I want to avoid using PRODRG because it is online which admins can easy see what I uploaded. I feel much more comfortable using programs on my system (the reason I am using acpype). Thanks again :) - Jonathan Saboury On Sat, Sep 21, 2013 at 12:06 PM, Jonathan Saboury jsab...@gmail.comwrote: I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- 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] Significant slowdown in 4.6? (4.6.3)
I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed and a desktop with an i3-3220 with 4.5.5 installed. I am trying the same energy minimization on each of these machines. My desktop takes a few seconds, my laptop takes hours. This doesn't make much sense bc benchmarks indicated that my laptop should be faster. Only conclusion I can come up with is that it is the difference in versions. Any other explanations? Here are the files I am using: http://www.sendspace.com/file/a1cdch List of commands used are found in: commands.txt I use the last command mdrun -v -deffnm em on each machine, and the files were built with 4.6.3 (my laptop). If you need any more information please let me know. Thank you! -Jonathan -- 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: Significant slowdown in 4.6? (4.6.3)
Figured out the problem. For some reason one thread is being taken up 90% by the system. If I run it with 6 threads it runs fast. Never experienced this on linux though, very curious. Sorry if i wasted your time. -Jonathan Saboury On Fri, Sep 20, 2013 at 7:58 AM, Jonathan Saboury jsab...@gmail.com wrote: I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed and a desktop with an i3-3220 with 4.5.5 installed. I am trying the same energy minimization on each of these machines. My desktop takes a few seconds, my laptop takes hours. This doesn't make much sense bc benchmarks indicated that my laptop should be faster. Only conclusion I can come up with is that it is the difference in versions. Any other explanations? Here are the files I am using: http://www.sendspace.com/file/a1cdch List of commands used are found in: commands.txt I use the last command mdrun -v -deffnm em on each machine, and the files were built with 4.6.3 (my laptop). If you need any more information please let me know. Thank you! -Jonathan -- 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] Invalid order for directive atomtypes
PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2 Commands used: http://pastebin.com/raw.php?i=YYG5ad7A Compressed folder containing all files (10.2 MB): http://www.sendspace.com/file/rka8ei So I want to simulate this complex. I am having problems with the .itp's and do not know why. I get the error: Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/topio.c, line: 656 Fatal error: Syntax error - File NAG_GMX.itp, line 3 Last line read: '[ atomtypes ]' Here is the logic I used while trying to get teh simulation to work, please let me know if this is correct, because there wasn't a tutorial example like this. 1.) Separate the complexed pdb into teh standard residues and ligands, so ATOM, HEM, NAG and S58in this case. 2.) There are multiple ligands in the pdb, so I need to delete all but one molecule and create a forcefield .itp so I can include it in the .top file. 3.) Once the .itp's for the single molecules are created, you need to put the complex back together. I was having problems with adding charges, so I only added hydrogen’s to the ligands and created complex.pdb from the new pdb files created from acpype. 4.) Minimize, relax waters, then simulate. So what did I do wrong here? Thanks!! :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Fatal error: number of coordinates in coordinate file (trp-b4ion.pdb, 25093) does not match topology (trp.top, 26684)
Files: http://www.sendspace.com/file/vxcnv3 Commands used: http://pastebin.com/raw.php?i=wPqfuUwc What I want to do: I just want to run the protein without the ligand in explicit water. Why is the coordinate file not matching topology? http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topologydoesn't offer much help in this case. I know the problem is the number of waters however. Thanks :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Limitations of simulations?
Alright, I think I have enough information now to play around with some settings! Thank you very much Justin, you have been very helpful :) -Jonathan -- View this message in context: http://gromacs.5086.x6.nabble.com/Limitations-of-simulations-tp5010100p5010147.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Fábio Filippi Matioli Unsubscribe
Look at the bottom on this page: http://lists.gromacs.org/mailman/listinfo/gmx-users -- 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] Limitations of simulations?
For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -Justin Do you think implicit water with 10-20 ligands would be able to do it? I see that the gpu accelerated implicit gets about 100-150 ns/day so a 10-20 day simulation would yield that time frame, no? Thanks :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
In an implicit, non-periodic system, it is more likely that the ligand will float away from the protein. I've tried it and that's all that ever happens. Moreover, the current Gromacs version does not support implicit solvent on GPU and the previous version that did had very limited functionality. -Justin Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? If so, does it give similar ns/day? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: editconf: Invalid command line argument: –f
Yep, the pdf was not written or copy and pasted the - incorrectly. Thanks :) -Jonathan On Fri, Jul 12, 2013 at 3:03 PM, Jonathan Saboury jsab...@gmail.com wrote: I am following Tutorial 1 from https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro but I get the error: Program editconf, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: –f Here are the files I am currently using: http://www.sendspace.com/file/a2twvx What is the problem? Thanks! -Jonathan -- 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] Limitations of simulations?
I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] editconf: Invalid command line argument: –f
I am following Tutorial 1 from https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro but I get the error: Program editconf, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: –f Here are the files I am currently using: http://www.sendspace.com/file/a2twvx What is the problem? Thanks! -Jonathan -- 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
