<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:18pt"><div><span><font size="3">What do you mean? Am I supposed to use C</font><font size="3">GenFF to derive parameters?</font></span></div><div><br><span></span></div><div><font size="3"><span>Cheers,</span></font></div><div><span><font size="3">Shima</font><br></span></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 18pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, May 9, 2012 5:20 AM<br> <b><span style="font-weight:
bold;">Subject:</span></b> Re: [gmx-users] Formyl parameters<br> </font> </div> <br>
<div id="yiv905598548">
<div>Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me...<br>
-- <br>
Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="yiv905598548gmail_quote">Shima Arasteh <shima_arasteh2001@yahoo.com> wrote:<blockquote class="yiv905598548gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex;">
<div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;"><div>Dear gmx users,</div><div><br></div><div>My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in <a target="_blank" href="http://gromacs.org">gromacs.org</a> , I need to include this .itp in .top file. How does it come when I have not got any .top file yet?</div><div>Anybody can suggest me how I can use .itp file and solve my problem?</div><div><br></div><div>Thanks in advance,</div><div>Shima</div></div></blockquote></div></div></div><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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