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
