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On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
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Dear Friends, <br>
Right now i am working on the docking of a small ligand to
a receptor. in order to begin md simulations in gromacs, i
need to create some files..<br>
<br>
I have already docked my ligand to the receptor and i have
those files:<br>
- ligand_receptor.gro<br>
- posre.itp (for only the receptor !!)<br>
<br>
<br>
I have 2 Questions:<br>
<br>
1- How can i expand the posre.itp file to also include the
ligand.data ? <br>
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<br>
Don't. The position restraints file is intended to be #included from
within a [moleculetype]. You have two, so you need two position
restraint files, each #included from a different, appropriate place.
The GROMACS tool genrestr can help generate that for the ligand.<br>
<br>
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<td style="font: inherit;" valign="top"> that means how
can i do to create a posre.itp-file for my
ligand_receptor-komplex ?<br>
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<br>
Don't.<br>
<br>
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2- I have 2 separate top-files: ligand.top (from the
prodrg-server) and the receptor.top file. How can i
"merge" the 2 files and obtain the file
ligand_receptor.top for the whole ligand-receptor-komplex
?<br>
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<br>
You need to convert one of your [moleculetype] definitions in one of
your .top files into an .itp file
(<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/File_Formats/.itp_File">http://www.gromacs.org/Documentation/File_Formats/.itp_File</a>) and
#include it suitably from the other. See chapter 5 of the manual for
details. This is tricky, do your homework first. Note that you
should take note of the warning here:
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Downloads/Related_Software/PRODRG">http://www.gromacs.org/Downloads/Related_Software/PRODRG</a><br>
<br>
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<br>
<br>
<br>
<br>
Many thanx, please email-me on my adress:
<a class="moz-txt-link-abbreviated" href="mailto:greendreams1983@yahoo.de">greendreams1983@yahoo.de</a><br>
<br>
Yours. <br>
<br>
<br>
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<br>
No, that is against accepted netiquette. If your question is worth
answering, then that answer is worth broadcasting and archiving so
others can learn from it.<br>
<br>
Mark<br>
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