Hi,<div>at the link <a 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 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><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? </div>
<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 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 href="http://convert_charmm_to_gromacs.pl" target="_blank">convert_charmm_to_gromacs.pl</a>
contained in the file charmm_to_gromacs.tgz (<a 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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