<div>Dear sir :</div> <div>Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore! <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 all users:<BR>> I want to simulate a system ( protein + chromophore). I <BR>> have had chromophore.gro and its top file using amb2gmx.pl,but I find I <BR>> can not use them to translate PDB( protein + chromophore) file into gro <BR>> and top files properly. So I need your advice about further procedure!<BR>> Thank you very much <BR><BR>You don't need a .gro file. See<BR>http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file<BR>The grompp utility will happily make a .tpr from your .mdp, your .top<BR>file, and your well-formed .pdb file whose atom, residue and
molecule<BR>names and ordering matches the .top file. This last constraint also<BR>applies to a .gro file!<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 gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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