<table cellspacing="0" cellpadding="0">
<tbody>
<tr>
<td><span style="COLOR: #00681c"><span style="PADDING-RIGHT: 1px; PADDING-LEFT: 0px; PADDING-BOTTOM: 1px; PADDING-TOP: 0px"></span></span>
<td style="PADDING-TOP: 0px" width="100%">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr>
<td>
<div><span><span></span></span> </div></td></tr></tbody></table>
<td style="PADDING-LEFT: 4px" align="right">
<div> </div>
<td align="right"></td></td></td></td></tr></tbody></table>
<div>Hi Servaas,</div>
<div> </div>
<div>Thanks for your reply. Your inforamtion is very helpful. Now I am trying to write the topology file by myself when dealing with a small molecule. I have know their conversion relationship, but in my case, I want to fix a few atoms in a plane. From the gaff.dat file , I can see the parameters on proper dihedral but not improper dihedral. I am just wondering how to retrival info. on improper dihedral from gaff.dat file. If you have such experience, please let me know. I do appreciate your kind help.</div>
<div> </div>
<div>best regards,</div>
<div> </div>
<div>Xiangyu</div>
<div><br><br> </div>
<div><span class="gmail_quote">On 3/14/08, <b class="gmail_sendername">servaas michielssens</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:servaas.michielssens@student.kuleuven.be" target="_blank">servaas.michielssens@student.kuleuven.be</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I don't think you can generate your topology from the pdb file with<br>gromacs in this case (with gaff). You can first make it in amber and<br>
than convert it to gromacs.<br>On this website is the info you need, in the FAQs there is a link to<br>dowload the script to do the job.<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://chemistry.csulb.edu/ffamber/" target="_blank">http://chemistry.csulb.edu/ffamber/</a><br>
<br><br>kind regards,<br><br>servaas<br><br><br><br>Date: Thu, 13 Mar 2008 22:57:29 -0400<br>From: "Xiangyu Fan" <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:xy.fan03@gmail.com" target="_blank">xy.fan03@gmail.com</a>><br>
Subject: [gmx-users] Help needed on using general amber force field<br> (GAFF) in Gromacs<br>To: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:7fb99dda0803131957p24274559vd3a29b0615484048@mail.gmail.com" target="_blank">7fb99dda0803131957p24274559vd3a29b0615484048@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi all,<br><br>I am using GAFF force field for Gromacs package to simulate MD of<br>surfactant<br>molecule. I know we can generate .top file using some simple command<br>
like<br>pdb2gmx if we use gromos force field. I am just wondering whether I can<br>do<br>the similar thing when using GAFF force field. If you have any<br>experience in<br>GAFF+Gromacs, please give me some advice. thanks<br>
<br>Xiangyu Fan<br><br>UNC-Chapel Hill<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL:<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/1cd1d95e/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/1cd1d95e/attachment-0001.html</a><br>
<br>------------------------------<br><br>Message: 6<br>Date: Fri, 14 Mar 2008 12:30:27 +0800<br>From: Yang Ye <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:leafyoung@yahoo.com" target="_blank">leafyoung@yahoo.com</a>><br>
Subject: Re: [gmx-users] Help needed on using general amber force<br> field (GAFF) in Gromacs<br>To: Discussion list for GROMACS users <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:47D9FF63.3080404@yahoo.com" target="_blank">47D9FF63.3080404@yahoo.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>You might not use pdb2gmx for such task.<br><br>Once you have generated topology in AMBER format with Antechamber in<br>GAFF, you will need to use some tools like ambconv.pl or ambconv (one<br>is<br>Perl script and one is a C++ programme, check GROMACS' website) to<br>
convert those files into GROMACS format.<br><br>There is ffamber, a port for AMBER force field to GROMACS, which<br>largely<br>similar to what ambconv.pl or ambconv produces. They will provide force<br>field for protein and nuclei acids through pdb2gmx. With some<br>
hand-modifications to the files, you can combine ambconv and ffamber,<br>so<br>you have a solution for almost all molecules.<br><br>Regards,<br>Yang Ye<br><br>Xiangyu Fan wrote:<br>> Hi all,<br>><br>> I am using GAFF force field for Gromacs package to simulate MD of<br>
> surfactant molecule. I know we can generate .top file using some<br>> simple command like pdb2gmx if we use gromos force field. I am just<br>> wondering whether I can do the similar thing when using GAFF force<br>
> field. If you have any experience in GAFF+Gromacs, please give me<br>some<br>> advice. thanks<br>><br>> Xiangyu Fan<br>><br>> UNC-Chapel Hill<br>><br>><br>><br>------------------------------------------------------------------------<br>
><br>> _______________________________________________<br>> gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br><br><br>
<br><br><br><br>_______________________________________________<br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div>
<br>