Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? Regards!
Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear sir : > Can you tell me a detail of procedure, I have only chromophore molecular > top,but I need entire top and gro for pdb + chromophore! Your use of terminology is unclear - and you can't afford this sort of lack of clarity in science. pdb, gro and top are all generic file formats. Your first email implied that you did have a file with your initial coordinates. The above implies the opposite. If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. I'd also suggest you follow Justin's advice, and do some tutorial material. If nothing else they should teach you by example some better ways of describing these things! :) Mark _______________________________________________ gmx-users mailing list gmx-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 --------------------------------- 雅虎邮箱传递新年祝福，个性贺卡送亲朋！
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