Re: [gmx-users] glutathionylation and SS bonds formation in GMX
Hi Luca, As Marc mentioned, they have to be recognized as one molecule (-merge). In addition, it is not just that the distance has to be less than that given in the specbond.dat file, it has to fall within a 10% range aruond that distance. Cheers, Tsjerk On 1/12/07, Marc F. Lensink <[EMAIL PROTECTED]> wrote: On Fri, Jan 12, 2007 at 04:08:47PM +0100, Luca Mollica wrote: > Dear GMX users, > > I am trying to simulate a post translational modification of a protein, > actually a glutathionylation of a Cys. I have tried a couple of times to > create a disulphide bridge between two Cys and I managed to do it without > troubles and simply manipulating a specond.dat file created in my working > directory. But in this case I am experiencing a slightly different trouble! > The Glutathione (GSH) has been built in Pymol manually (Cys + Gly + Glu) > and the coordinates have been saved for keeping it close to the desired > Cys, with S - S distance less than how indicated in specbond.dat). So far > so good, everything in molecular structure was OK ... the troubles started > using GMX, when the two Cys were recognized, specbond.dat was read > correctly, but no bond was created. Actually, the protein and GSH remained > separated and there was no chance to make them bound through a disulphide > bridge. I even tried to give a cahin identifier to protein (A) and GSH (B), > but I got the same result: two separated units, no SS bond ! > > Do you have any suggestion about this issue ? I am pretty sure that in the > past I got a certain degree of success because the Cys considered were part > of the same molecule, actually. But I cannot get the point for this failure > in the system building process. isn't there some option to merge (-merge) molecules in pdb2gmx? i suppose you should also make sure that the atoms have the correct names. cheers, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] infinitive force acting on atom during minimization
Hi Joern, Did you first perform an energy minimization in vacuum? The values you get indicate severe problems with your starting structure. By the way, for such a system you don't want to use a cubic box. It's an utter waste of resources. You're better off with a rhombic dodecahedron, or you can contact me off list if you want to cut your volume by half and still have the same distance between periodic images (right, speed up your simulations >2*). Cheers, Tsjerk On 1/12/07, Joern Lenz <[EMAIL PROTECTED]> wrote: dear users, i try to simulate a system of DNA (17 bp) and a protein (420 aa). before i start my MD runs, i solvated the system in a cubic box (-d = 0.9) and started a minimization of it using the em.mdp file which you can see at the bottom of this email. unfortunately the minimization breaks (see below). And if it does not break, it is very slow (20 iterations take about 3 weeks). Can you see from the information i give to you, why this happens? The output of this minimizations looks something like: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 400 Step=0, Dmax= 5.0e-04 nm, Epot= 4.14463e+16 Fmax= inf, atom= 2005 Step=1, Dmax= 5.0e-04 nm, Epot= nan Fmax= 0.0e+00, atom= 0 Step=2, Dmax= 2.5e-04 nm, Epot= nan Fmax= 0.0e+00, atom= 0 Step=3, Dmax= 1.3e-04 nm, Epot= nan Fmax= 0.0e+00, atom= 0 Step=4, Dmax= 6.3e-05 nm, Epot= nan Fmax= 0.0e+00, atom= 0 ... Hence there is an infinitive force acting on atom 2005 in my system, right ? First I looked at the coresponding file to figure ot which residue this atom belongs to. I then looked at the system using chimera as a viewer and found that is residue occurs several times in my system, which worries me a little bit. But there is no such thing like two atoms lying very close to each other which would explain the Fmax= inf, atom= 2005 line in the minimization. Has anyone got an idea of what is going wrong here or do you need more information about my used files. It would be of great help for my further work, so thanks a lot in advance and have a nice weekend Greetings em.mdp: title = Minimization of blah.pdb cpp = /usr/bin/cpp define = -DFLEX_SPC integrator = steep nsteps = 400 nstenergy = 5 nstxtcout = 5 nstlist = 5 ns_type = simple rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraints = none emtol = 1.0 emstep = 0.005 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation error (core dump)
> Dear gmx-users, > > I installed the gromacs-3.3.1 on Cygwin and no problems occured, but when > I execute the commands such as g_angle,pdb2gmx, all commands gave the > message: Segmentation fault (core dumped) at the end. Anybody have met > this problem ever? How to resolve it? > Thanks for any advises. Something's badly broken. I would recommend a clean install of both cygwin and gromacs (search the mailing list for my gromacs-cygwin HOWTO for some tips) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Has the forces for virtual sites in the trr filebeen reditributed?
Yes they have. You can also see that the force on the virtual site is zero. Got it! Thanks a lot _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
I've rerun everything from scratch following Bert's input. The numbers seemed all right, but the runs still failed. Then I tried using just a subset of the eigenvectors, which has worked so far (i.e. it's running for about 1ns). Bert and Lars - thanks a lot for your help, Ran. Bert de Groot wrote: > > then there's possibly some mixup between fitting reference and/or > selection > and/or the eigenvectors between g_anaeig and make_edi? > > Please make sure that group selections and reference groups (-s option > of make_edi, g_covar and g_anaeig) are identical. Check covar.log if > you're > not sure anymore which fitting structure/selection you chose for g_covar. > > If you still have problems, please feel free to contact me off-list > with a minimal > set of files with which the problem can be reproduced. > > cheers, > > Bert > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
