Thanks for the kindly replies. I write a python script to remove the water and then substitute the ion with TMA, Then add water again. If I only add several TMA, It work well. Otherwise, the box have to enlarged, since the atoms went out of the box.
Then I find -ci option of the genbox may be work for me. It seem work. When I run an em on this system, no strange problem rise. although The density was a little large when more TMA were added in. It's not a big problem, which can solve with pressure coupled equilibrium. It seem the problem is not difficult as I mentioned before. Is the method with genbox good enough? simple > Another approach to adding it might be to take your protein, before > solvating it, and write a script to add some number of TMA molecules > randomly distributed throughout the box. Then solvate in the usual > way. This obviously would take some work, though. > > David > > On 3/14/06, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Simple wrote: > > > In chemical experiments that ion effect is > > > important,tetramethylammonium (TMA) is usually added to compensate the > > > ion strength.I would like to test it in simulation. There were > > > experiments showed that the ion contributed a lot to the distinct > > > results. > > > I looked around but not found a topology of TMA is ready-to-use. So > > > I decided to create one. Thanks for Schuettelkopf and van Aalten, The > > > PRODRG server do all the things. Since I am still a newbie for Gromacs > > > and not very confident with my chemistry knowledge,I wonder if the > > > parameters in the topology is rational? (The topology is present at the > > > last.) > > > > compare it to topologies for lipid headgroups available from the > > Tieleman website > > > > > The second problem is how can I use this topology as a general ion. > > > It is difficult to add them into gro file by hand because I should > > > put a lot of TMA into the solutions. > > > > genion will not be able to handle this because it is too big (genion > > replaces water molecules by ions). You will need to use e.g. genconf > > and/or genbox, but there is no ready solution. Maybe you can do a simple > > simulation of a TMA solution and then dissolve the protein in that. > > > > > If I can treat it as a general ion, such as Na or Mg,etc, which will > > > save me a lot. My straight forward thought is to add the information > > > into the ion.itp, so genion can find and use it. If this work, I > > > believe others would also benefit from it, since TMA is so widely used. > > > Does it work well? If this method is not so good,I think I can write a > > > simple program to substitute the ion in the gro with TMA. Of course, I > > > would rewrite the position of all the TMA atom and renumber the atom. > > > For the top file, I need only replace the ion name with TMA. > > > What should I pay a lot of attention to for these method? > > > > > > If something I wrote are totally wrong, please not hesitate to let > > > me know. Thanks. > > > > > > topology created by PRODRG > > > ; > > > ; This file was generated by PRODRG version 051202.0518 > > > ; PRODRG written/copyrighted by Daan van Aalten > > > ; > > > ; Questions/comments to [EMAIL PROTECTED] > > > ; > > > ; When using this software in a publication, cite: > > > ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). > > > ; PRODRG - a tool for high-throughput crystallography > > > ; of protein-ligand complexes. > > > ; Acta Crystallogr. D60, 1355--1363. > > > ; > > > ; > > > > > > [ moleculetype ] > > > ; Name nrexcl > > > TMA 3 > > > > > > [ atoms ] > > > ; nr type resnr resid atom cgnr charge mass > > > 1 CH3 1 TMA C1 1 0.076 15.0350 > > > 2 NL 1 TMA N1 1 0.696 14.0067 > > > 3 CH3 1 TMA C3 1 0.076 15.0350 > > > 4 CH3 1 TMA C4 1 0.076 15.0350 > > > 5 CH3 1 TMA C2 1 0.076 15.0350 > > > > > > [ bonds ] > > > ; ai aj fu c0, c1, ... > > > 1 2 1 0.147 376560.0 0.147 376560.0 ; C1 N1 > > > 2 3 1 0.147 376560.0 0.147 376560.0 ; N1 C3 > > > 2 4 1 0.147 376560.0 0.147 376560.0 ; N1 C4 > > > 2 5 1 0.147 376560.0 0.147 376560.0 ; N1 C2 > > > > > > [ pairs ] > > > ; ai aj fu c0, c1, ... > > > > > > [ angles ] > > > ; ai aj ak fu c0, c1, ... > > > 1 2 3 1 109.5 376.6 109.5 376.6 ; C1 N1 > > > C3 1 2 4 1 109.5 376.6 109.5 376.6 ; C1 > > > N1 C4 1 2 5 1 109.5 376.6 109.5 376.6 ; C1 > > > N1 C2 3 2 4 1 109.5 376.6 109.5 376.6 ; > > > C3 N1 C4 3 2 5 1 109.5 376.6 109.5 376.6 ; > > > C3 N1 C2 4 2 5 1 109.5 376.6 109.5 376.6 > > > ; C4 N1 C2 > > > > > > [ dihedrals ] > > > ; ai aj ak al fu c0, c1, m, ... > > > 2 1 3 4 2 35.3 836.8 35.3 836.8 ; imp N1 > > > C1 C3 C4 > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > 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 > > > > -- > > David. > > ________________________________________________________________________ > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: 46 18 471 4205 fax: 46 18 511 755 > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > _______________________________________________ > gmx-users mailing list [email protected] > 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 _______________________________________________ gmx-users mailing list [email protected] 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
