Re: [gmx-users] g_anaeig pymol
Hi, you probably did the covariance analysis on the backbone atoms of your system. However, for the calculation of the secondary structure PyMOL needs at least the MainChain part of your molecule. So the easiest thing would be repeat your analysis with the MainChain group instead of backone. D. On Wednesday 07 July 2010 10:37:06 am Carla Jamous wrote: Hi everyone, I did a covariance analysis by following this link: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html Now I want to visualize the differences between the extreme structures by doing this: pymol ev?.pdb Split the models in the pdb files and delete the originals. split_states ev1 split_states ev2 delete ev1 or ev2 Colour the models. This will result in the extreme structures from eigenvector 1 to be displayed in blue-green and those from eigenvector two in yellow-red. Then display them in cartoon representation. spectrum count dss hide everything show cartoon But I encountered a problem: When I do dss, pymol sends me this error message: AssignSS-Warning: Ignoring incomplete residue ev3_apo_0002//B/218/.. for all the residues. And afterwards, I can't visualize the structures in cartoon representation. Please does anyone have an idea what is the problem? PS: the 5 first eigenvectors don't account for 80% of the total motility, so could this be my problem? Thank you, Carla -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Free Energy calculations of peptide-protein binding
Hi Ehud, we recently developed an extended amber99sb forcefield + some scripts which probably can do exactly what you want (setting up alchemical mutations for any amino acid mutation except for proline). We tested it by calculating thermostability differences for a set of 100+ mutations of an enzyme and got quite accurate agreement with experimental data (R=0.86 ). If you want I can send you the stuff you need to set up the simulations. Details about simulation parameters you can find in the paper. ( http://www.cell.com/biophysj/abstract/S0006-3495%2810%2900216-X ) In general I would not use a plain thermodynamic integration scheme because it does not converge very well, especially for large mutations. We used a Crooks-based non-equilibrium scheme which worked quite well but there are also other protocols around (multi-state BAR) which probably do equally well. -Daniel On Monday 05 July 2010 04:35:17 pm Ehud Schreiber wrote: Dear GROMACS users, I am investigating a certain peptide which is well bound to some protein; their configuration is known from the PDB. My aim is to compare the binding free energies of several variants of the peptide. In particular, I wish to mutate some amino acids to others. I have read some tutorials and mailing list messages; still, I have several questions unanswered. I plan to use the Thermodynamic Integration (TI) method in an alchemical setting, in which I turn off the side chain. The naked amino acid will then be my reference point comparing to real amino acids. In this way I should be able to obtain, using the usual thermodynamical cycle, the binding free energy difference of two amino acids (Delta Delta G), which is sufficient for my needs and should be more accurate than computing absolute binding free energies (Delta G). 1) Does this sound like the best approach? 2) In particular, is it O.K. to use a naked amino acid (with no side chain at all) as the reference, or should Glycine or Alanine be used? 3) Following the above procedure, I still would not achieve a naked amino acid. Rather, a side chain ghost remains, non-interacting but still bonded to itself and to the C-alpha. Is it correct to assume that the contribution of such a ghost would cancel between the free and bound peptide? 4) Are the OPLS-AA force field, theTIP-3P water model and the NpT ensemble good choices? I have seen two methods used to make the change between the initial and final states. The first (and simplest) is to use the couple-moltype parameter of mdrun. However, this seems to change a whole molecule, while I'm interested in changing only a part (the side chain). 5) Can I define the side chain and the amino acid backbone as different molecules, and change the former, still connecting them one to the other? Alternatively, the topology of the B state can be explicitly provided (as described e.g. in section 5.7.4 of the version 4.0 user manual). 6) The atom charges can be specified for state B, as appropriate for turning off the Coulomb interactions. In order to turn off the vdW ones, must I define new atom types? 7) Are there perhaps such amino acid variants already built? Finally, some technicalities: 8) I have seen the sc-alpha parameter (when sc-power = 1) given the values 1.0, 0.7 and 0.5. What is recommended? 9) Should I employ DispCorr = EnerPres ? Thanks, Ehud Schreiber. -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define
Hi, I also encoutered a strange behaviour of gmxcpp when using B-states. When I set up up a free energy simulation (gromacs 4.0.2) with amber03 (ffamber from Sorin Pande), I define a dihedral angle, e.g. like [ dihedrals ] . 511 515 517 513 3 aromatic_prop_5aaromatic_prop_5 . If I process this topology with grompp it claims that there is no B-state defined. In the original ffamber03bon.itp there were comments in the define lines, e.g. #define aromatic_prop_5 41.84000 0.0 -41.84000 0.0 0.0 0.0 ; X-CR-NB-X (HIX) These were already removed since this causes grompp to cut the line after the first ; and, hence it ignores the B-values. Now the strange thing: This works for all defined dihedrals except for those that end with an a. So: 12 3 4 aromatic_prop_4 aromatic_prop_5 works fine, but 12 3 4 aromatic_prop_5a aromatic_prop_5 doesn't work. If I look into the processed topology, grompp has converted the first define, but not the second one. If I exchange the two dihedrals, like 12 3 4 aromatic_prop_5 aromatic_prop_5a it works again. I get the error only when these dihedrals are in the A-state: aromatic_prop_4a aromatic_prop_5a aromatic_prop_6a If I preprocess my topology with cpp -traditional all defines are nicely converted, so I guess there must go sth. wrong in gmxcpp. I also tried the fixed version from Berk as pointed out before, but this didn't do the job. Thanks, Daniel On Tuesday 25 November 2008 23:34:24 Berk Hess wrote: Hi, That is an annoying bug. I fixed it for 4.0.3. If you want it fixed now, the diff is below. Berk RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v retrieving revision 1.9 diff -r1.9 gmxcpp.c 121,122c121,122 sscanf(define,%s,name); ptr = define + strlen(name); --- sscanf(define,%s%n,name,i); ptr = define + i; Date: Tue, 25 Nov 2008 16:32:57 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define When two spaces are included the #define KEYWORD is incompletely removed from the file. In case my conclusion about the exact nature of the error is incorrect, here is more information. I have a ffcharmbon.itp file that contains: [ dihedraltypes ] #define improper_NC2_X_X_C_ 180.0 83.68000 2 And an .itp file that contains: [ dihedrals ] 1 2 5 8 1 improper_NC2_X_X_C_ where grompp -pp returns [ dihedrals ] 1 2 5 8 1 _ 180.0 83.68000 2 and the floating '_' character causes the error message: ERROR 1 [file my.itp, line 77]: No default Proper Dih. types I tried to fix this by removing the trailing underscore character from my defined string in both files, but now I get a trailing 'C' [ dihedrals ] 1 2 5 8 1 C 180.0 83.68000 2 So it appears that the define statement is simply not being entirely removed. When I then replaced #define improper_NC2_X_X_C_ 180.0 83.68000 2 by #define improper_NC2_X_X_C_ 180.0 83.68000 2 (only one space between '#define' and 'improper...') it works correctly. Note that cpp handled this original define statement properly in gromacs 3.3.1. Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: [EMAIL PROTECTED] www.mpibpc.mpg.de/groups/de_groot/dseelig/index.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
