[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

[gmx-users] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)

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

[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

[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

[gmx-users] Funky output trajectory (lines all over the place)

, 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

[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

[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

[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

[gmx-users] Re: No such moleculetype SOL

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

[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

[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

[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

[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?

[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

[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

[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

[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.

[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

[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

[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: