Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? <BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> 写道： <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">xi zhao wrote:<BR>> Dear sir :<BR>> In fact, I have a complex structure(which contains protein and <BR>> chromophore), though I have known the usual procedure dealing with <BR>> ligand or drug in the gromacs, such as Prodrg server. Now I want to use <BR>> Amber force field, and must deal with chromophore molecule in the <BR>> complex using amb2gmx.pl, then have chromophore.gro and top file. But <BR>> when the simulation runs, I need a complex entire gro and top files in <BR>> order to run, but I do not know how to use existing top and gro files to <BR>> produce entire gro and top . Are you
clear?<BR><BR>> 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>It sounds like my earlier advice is appropriate. If you need to insert<BR>your chromophore into your protein to form a complex to give yourself an<BR>initial structure, then you will need to choose that protein structure<BR>in a suitable conformation (this is not trivial) and then to "dock" that<BR>chromophore. How easy it is to do the latter will depend on your<BR>available experimental information. Google (or scientific literature)<BR>searching for "docking" and "model building" is your best bet here -<BR>it's well outside the scope of the GROMACS tool set.<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
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