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On 18/05/2012 8:02 PM, francesco oteri wrote:
<blockquote
cite="mid:CAFQcp-OuO57tKVUh3NNBjLgFW23nR7Gn+AJ8YB+YdH=xexfx7g@mail.gmail.com"
type="cite">Hi,
<div>at the link <a moz-do-not-send="true"
href="http://dl.dropbox.com/u/40545409/charmm2itp.tgz"
target="_blank">http://dl.dropbox.com/u/40545409/charmm2itp.tgz</a>
you can find the files I am using</div>
<div><br>
Files ffcharmmnb.itp ffcharmmbon.itp have been generated
through:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://convert_charmm_to_gromacs.pl/" target="_blank">convert_charmm_to_gromacs.pl</a> par_all36_carb.prm</div>
<div><br>
</div>
<div>while carbohydrates.rtp and carbohydrates.rtp through a
script of mine.</div>
<div><br>
</div>
<div>Now, if you look at [ dihedraltypes ] section in file
ffcharmmbon.itp, there are strange things:</div>
<div><br>
</div>
<div>1) dihedrals defined once, are converted Ryckaert-Bellemans
form, while the armonic form should be more clear. </div>
<div> Anyway, it just a matter of style so I dont complan
about.</div>
<div><br>
</div>
<div>2) dihedrals with multiple definitions ( OC30P CC3162 CC3161
OC311 at line 598 in file ffcharmmbon.itp, for example) are
defined as:</div>
<div> OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84
0 0</div>
<div>; 30P CC3162 CC3161 OC311 1 180 10.46 1</div>
<div>; 30P CC3162 CC3161 OC311 1 0 8.368 2</div>
<div>; 30P CC3162 CC3161 OC311 1 0 10.46 3</div>
<div><br>
</div>
<div>The commented lines clearly display the multiple definition,
that can be described using function 9</div>
</blockquote>
<br>
... which didn't exist at the time of my writing of that script, as
the comments in the script discuss. Hence solution 1), which was
adequate for the subset of CHARMM27 that was of interest to me.<br>
<br>
<blockquote
cite="mid:CAFQcp-OuO57tKVUh3NNBjLgFW23nR7Gn+AJ8YB+YdH=xexfx7g@mail.gmail.com"
type="cite">
<div><br>
</div>
<div><br>
</div>
<div>3) An other problem rise with impropers dihedrals. Any of
them are defined as Ryckaert-Bellemans, </div>
<div>ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0</div>
<div>at line 926 of ffcharmmbon.itp</div>
<div><br>
</div>
<div>while points 1 and 2 don't impact on the correctness of the
simulation and can be bypassed defining </div>
<div>[ bondedtypes ] section as following </div>
<div><br>
</div>
<div>1 5 3 2 1 3 1
0 </div>
<div><br>
</div>
<div>Problem 3 cannot be solved without manipulating
the ffcharmmbon.itp. </div>
<div>In fact, since some impropers are defined as functiontype 2
other as functiontype 3, </div>
<div>so there is not an unique bondedtypes definition covering
both the definition.</div>
<div><br>
</div>
<div>Did I any mistake or actually there is a problem in the
script? <br>
</div>
</blockquote>
<br>
IIRC CHARMM36 is more recent than that script, so the assumptions
made by the script for CHARMM27 may not be applicable. If CHARMM36
uses more than one kind of improper dihedral, then I would not
expect the script to function correctly in this regard. You would
need to modify the script or its output.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFQcp-OuO57tKVUh3NNBjLgFW23nR7Gn+AJ8YB+YdH=xexfx7g@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>Francesco</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div class="gmail_quote">2012/5/18 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>
<div> On 18/05/2012 2:52 AM, francesco oteri wrote:
<blockquote type="cite">Dear gromacs users,
<div>I am trying to port a set of charm parameter in
gromacs. </div>
<div><br>
</div>
<div>I am using the script <a moz-do-not-send="true"
href="http://convert_charmm_to_gromacs.pl"
target="_blank">convert_charmm_to_gromacs.pl</a>
contained in the file charmm_to_gromacs.tgz (<a
moz-do-not-send="true"
href="http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz"
target="_blank">http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz</a>).</div>
<div><br>
</div>
<div>Regarding dihedrals, the entry regarding the file
says that pdb2gmx cannot</div>
<div><br>
</div>
<div><span
style="line-height:17px;color:rgb(79,107,114);font-size:12px;font-family:arial,verdana,helvetica">"generate
multiple periodic dihedral functions such as
CHARMM uses for some dihedrals - </span></div>
<div><span
style="line-height:17px;color:rgb(79,107,114);font-size:12px;font-family:arial,verdana,helvetica">these
must be converted to Ryckaert-Bellemans functions,
i.e. expressed as a cosine power expansion"</span></div>
<div><br>
</div>
<div>
<div>This assumption is no longer valid, is it?</div>
<div>As far as I know, infact, now gromacs support
multiple periodic function (funtion 9), is it?</div>
<br>
</div>
</blockquote>
<br>
</div>
</div>
Correct, but with the inclusion of native CHARMM27 in
GROMACS, I have had no reason to upgrade these conversion
scripts to support function type 9.<span><font
color="#888888"><br>
<br>
Mark<br>
</font></span></div>
<br>
--<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Cordiali saluti, Dr.Oteri Francesco<br>
<br>
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</blockquote>
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