[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, l

[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 wrote: > I am following "Tutorial 1" from > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html > > I try t

[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

[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 d

[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 suffic

[gmx-users] Re: Limitations of simulations?

Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? -- View this message in context: http://gromacs.5086.x6.nabble.com/Limitations-of-simulations-tp5010100p5010103.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

[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 functionali

[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 User

[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_coordi

[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 w

[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 indicat

[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 wrote: >

[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 e

[gmx-users] Re: No such moleculetype SOL

ee 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 wrote: > I am doing this tutorial: > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-

[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 s

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

ed :/ 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)

[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,

[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 assum

[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 h

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

emistry 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!

[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