<DIV>Dear sir :</DIV> <DIV>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?</DIV> <DIV>Regards! <BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> 写道:</DIV> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">xi zhao wrote:<BR>> Dear sir :<BR>> Can you tell me a detail of procedure, I have only chromophore molecular <BR>> top,but I need entire top and
gro for pdb + chromophore! <BR><BR>Your use of terminology is unclear - and you can't afford this sort of<BR>lack of clarity in science. pdb, gro and top are all generic file<BR>formats. Your first email implied that you did have a file with your<BR>initial coordinates. The above implies the opposite. If you lack a file<BR>containing your initial coordinates, then you may need to do some<BR>serious leg-work to get one, e.g. search the Protein Data Bank.<BR><BR>I'd also suggest you follow Justin's advice, and do some tutorial<BR>material. If nothing else they should teach you by example some better<BR>ways of describing these things! :)<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to
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