<div>Dear sir:</div> <div>Is my english weak? I want to simulate pdb:1O5P (<A href="http://www.rcsb.org">www.rcsb.org</A>), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system.<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>> Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding <BR>> gro top files, but I can only produce chromophore gro and top file using <BR>> amb2gmx.pl .Are you clear ? <BR><BR>No. If you have a structure file already, then you need to read what I<BR>wrote earlier. If you don't have a structure file already, then you need<BR>to read what I wrote
earlier. If you have some problem getting an<BR>existing AMBER structure+prmtop to convert properly, then you haven't<BR>communicated that. If you haven't got an AMBER structure+prmtop, then<BR>give up on amb2gmx.pl<BR><BR>Try explaining your problem in English to a friend who doesn't fully<BR>understand the science. Then apply the lessons you learned there to<BR>describing the problem here :-)<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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