Hi Par Bjelkmar,<div><br></div><div><div><br></div><div>I need to do an all atom simulation for dppc bilayer . You are right the dppc molecule file that i have has PALM and PCGL residues. </div><div><br></div><div>I will like to try to set up the charmm FF for gromacs. But I dont have the FF files with me, neither do i have the programs. Could you send me a tutorial or some reference link too ( if you know of any).</div>
<div><br></div><div>Thank you,</div><div>Amit</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Thu, Oct 15, 2009 at 4:01 AM, Pär Bjelkmar <span dir="ltr"><<a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word"><div>Hi,</div><div><br></div><div><div>15 okt 2009 kl. 07.08 skrev <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>:</div>
<blockquote type="cite"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:medium;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br>
<blockquote type="cite">The reason I am asking this is because it will require me to create<span> </span><br></blockquote><blockquote type="cite">gromacs compatible FF files of the Charmm FF . I did find two perl<span> </span><br>
</blockquote><blockquote type="cite">scripts which can do probably handle that but i am wondering if the<span> </span><br></blockquote><blockquote type="cite">compatible FF are already up on gromacs website somewhere.<br>
</blockquote></span></blockquote><div>No, it is not available on the gromacs website yet. You can get the current parameter files from me if you'd like to try it out. I'm afraid the DPPC lipid in CHARMM is created by combining the PALM and PCGL residues and some patches so if you know how that works in CHARMM you might be able to create the DPPC residue. </div>
<div><br></div><blockquote type="cite"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:medium;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><blockquote type="cite">
<br></blockquote><br>No one ever said life was easy :) CHARMM support is under development, you can<span> </span><br>get the source via the git repositories, but I don't know its current status.<br></span></blockquote>
<div>As Justin is saying, CHARMM will be supported as of version 4.1. The source code is there in git master branch but you need to get the ff files from me. </div><div><br></div><blockquote type="cite"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:medium;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><blockquote type="cite">
<font color="#000000"><br></font></blockquote><blockquote type="cite"> I have been trying to search for an all atom DPPC sructure<br></blockquote><blockquote type="cite"> (including the missing Hydrogens of long chain hydrocarbons) and<br>
</blockquote><blockquote type="cite"> then do an all atoms md simulation on it. I havent yet found any<br></blockquote><blockquote type="cite"> such structure or any force field that could be used for it on the<br></blockquote>
<blockquote type="cite"> internet. Is anybody familiar with any such work ?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Is there any all atom model for hydrocarbons which is incorporated<br>
</blockquote><blockquote type="cite"> in Gromacs? I am not 100 % sure about it.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> I want to do this to parametrize another force field which<br>
</blockquote><blockquote type="cite"> essentially uses all atom model.<br></blockquote></span></blockquote></div><br><div><div>/Pär Bjelkmar</div><div><br></div><blockquote type="cite"><span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:medium;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"></span></blockquote>
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<div><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3"><><><><><><><><><><><><><><><><><><></font></p>
<p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">Pär Bjelkmar, PhD student<span style="white-space:pre"> </span></font></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
<br></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">Stockholm Center for Biomembrane Research,</font></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Stockholm Bioinformatics Center,</p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">Department of Biochemistry and Biophysics,</p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Stockholm University</p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><br></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">Tel:<span> </span><span style="white-space:pre"> </span>+46-8-16 2746<span style="white-space:pre"> </span><span style="white-space:pre"> </span><span style="white-space:pre"> </span></font></p>
<p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">Fax:<span> </span>+46-8-15 3679<span style="white-space:pre"> </span><span style="white-space:pre"> </span><span style="white-space:pre"> </span></font></p>
<p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">E-mail: <a href="mailto:bjelkmar@cbr.su.se" target="_blank">bjelkmar@cbr.su.se</a><span style="white-space:pre"> </span><span style="white-space:pre"></span></font></p>
<p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font face="Helvetica" size="3">Home: <span style="white-space:pre"><span style="white-space:normal"><a href="http://www.dbb.su.se/User:Bjelkmar" target="_blank">http://www.dbb.su.se/User:Bjelkmar</a><span style="white-space:pre"> </span><span style="white-space:pre"> </span></span></span></font></p>
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