Thank you so much for your kind helps. did you pre-equilibrium it?<br><br>At 2011-05-30,"Jianguo&nbsp;Li"&nbsp;&lt;ljggmx@yahoo.com.sg&gt; wrote:<br> <BLOCKQUOTE id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi Albert,<br><br>Here is one gro file of 128 POPC lipids which I constructed before using CHARMM36 FF. please check if it is correct before using it. <br><br>Jianguo<br>&nbsp;<br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> albert &lt;<A href="mailto:leuven@yeah.net">leuven@yeah.net</A>&gt;<br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users &lt;<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>&gt;<br><b><span style="font-weight: bold;">Sent:</span></b> Monday, 30 May 2011 14:12:19<br><b><span style="font-weight: bold;">Subject:</span></b> Re:Re: [gmx-users] is it possible to convert NAMD psf file to
 gromacas format?<br></font><br>Thank you very much for your kind reply.<br>The problem is that there are too many atom names for 72 full atom lips and it can make mistakes easily.<br>If a rename atom A into B, it will mix the old atom B which already there before A renamed into B. However, if the old atom B also need to be renamed into C. Here is the problem , command cannot recognize this atom B is the new generated or the old atom B. Of course, those atom B derive from A should not be renamed into C..... <br><br>If there is only dozens of atoms name, it would be ok modify them manually. But if there are thousands, it would be a big problem to do so. <br><br><br>THX<br><div></div><br><pre><br><span>At&nbsp;2011-05-30,"Francesco&nbsp;Oteri"&nbsp;<francesco.oteri>&nbsp;wrote:

&gt;I&nbsp;guess&nbsp;it&nbsp;is&nbsp;tedious&nbsp;but,&nbsp;in&nbsp;my&nbsp;opinion&nbsp;it&nbsp;is&nbsp;more&nbsp;correct&nbsp;changing&nbsp;the&nbsp;
&gt;atom&nbsp;name&nbsp;in&nbsp;the&nbsp;pdb&nbsp;and&nbsp;using&nbsp;gromacs&nbsp;topology&nbsp;generation&nbsp;tools.&nbsp;So&nbsp;you&nbsp;
&gt;are&nbsp;sure&nbsp;the&nbsp;topology&nbsp;will&nbsp;be&nbsp;suitable&nbsp;for&nbsp;gromacs&nbsp;simulation.
&gt;
&gt;You&nbsp;rename&nbsp;atom,&nbsp;using&nbsp;the&nbsp;command&nbsp;sed.
&gt;In&nbsp;particular:
&gt;
&gt;sed&nbsp;"s/old/new/g"&nbsp;file
&gt;
&gt;replaces&nbsp;each&nbsp;occurence&nbsp;of&nbsp;"old"&nbsp;with&nbsp;"new".&nbsp;Once&nbsp;you&nbsp;find&nbsp;the&nbsp;
&gt;correspondenze&nbsp;between&nbsp;gromacs&nbsp;and&nbsp;pdb&nbsp;atom&nbsp;name,&nbsp;you&nbsp;can&nbsp;solve&nbsp;the&nbsp;
&gt;problem.
&gt;
&gt;
&gt;Alternatively,you&nbsp;can&nbsp;replace&nbsp;atom&nbsp;name&nbsp;using&nbsp;some&nbsp;text&nbsp;file&nbsp;editor.
&gt;
&gt;
&gt;
&gt;
&gt;Il&nbsp;29/05/2011&nbsp;22:35,&nbsp;albert&nbsp;ha&nbsp;scritto:
&gt;&gt;&nbsp;Well,&nbsp;I&nbsp;also&nbsp;try&nbsp;to&nbsp;do&nbsp;this.&nbsp;But&nbsp;it&nbsp;seem&nbsp;that&nbsp;the&nbsp;atom&nbsp;name&nbsp;in&nbsp;my&nbsp;POPC&nbsp;
&gt;&gt;&nbsp;pdb&nbsp;file&nbsp;(which&nbsp;I&nbsp;download&nbsp;from&nbsp;here&nbsp;
&gt;&gt;&nbsp;<a target="_blank" href="http://terpconnect.umd.edu/%7Ejbklauda/research/download.html">http://terpconnect.umd.edu/~jbklauda/research/download.html</a>&nbsp;)&nbsp;is&nbsp;
&gt;&gt;&nbsp;different&nbsp;from&nbsp;the&nbsp;the&nbsp;one&nbsp;in&nbsp;Gromacs&nbsp;topol&nbsp;database.&nbsp;There&nbsp;are&nbsp;72&nbsp;
&gt;&gt;&nbsp;lips&nbsp;in&nbsp;the&nbsp;system&nbsp;in&nbsp;all.&nbsp;So,&nbsp;it&nbsp;would&nbsp;be&nbsp;very&nbsp;difficult&nbsp;to&nbsp;modify&nbsp;
&gt;&gt;&nbsp;them&nbsp;one&nbsp;by&nbsp;one.
&gt;&gt;
&gt;&gt;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much
&gt;&gt;
&gt;&gt;&nbsp;At&nbsp;2011-05-30,"Francesco&nbsp;Oteri"<francesco.oteri>&nbsp;&nbsp;wrote:
&gt;&gt;
&gt;&gt;&nbsp;&gt;You&nbsp;can&nbsp;solve&nbsp;the&nbsp;problem&nbsp;without&nbsp;converting&nbsp;from&nbsp;namd&nbsp;to&nbsp;gromacs.
&gt;&gt;&nbsp;&gt;You&nbsp;can&nbsp;use&nbsp;the&nbsp;pdb&nbsp;you've&nbsp;already&nbsp;found&nbsp;to&nbsp;obtain&nbsp;a&nbsp;valid&nbsp;gromacs
&gt;&gt;&nbsp;&gt;topology&nbsp;through&nbsp;pdb2gmx
&gt;&gt;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;Il&nbsp;29/05/2011&nbsp;22:24,&nbsp;albert&nbsp;ha&nbsp;scritto:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much&nbsp;for&nbsp;kind&nbsp;messages.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;I&nbsp;am&nbsp;trying&nbsp;to&nbsp;convert&nbsp;a&nbsp;membrane&nbsp;system&nbsp;psf&nbsp;file&nbsp;for&nbsp;gromcas&nbsp;MD
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;simulation.&nbsp;For&nbsp;I&nbsp;would&nbsp;like&nbsp;to&nbsp;use&nbsp;CHARMM36&nbsp;for&nbsp;my&nbsp;POPC&nbsp;system,&nbsp;but&nbsp;I
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;cannot&nbsp;find&nbsp;pre-equilibrium&nbsp;CAHRMM36&nbsp;based&nbsp;POPC&nbsp;system.&nbsp;However,&nbsp;there
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;is&nbsp;some&nbsp;for&nbsp;NAMD&nbsp;and&nbsp;I&nbsp;download&nbsp;the&nbsp;pdf&nbsp;and&nbsp;psf&nbsp;file&nbsp;hoping&nbsp;that&nbsp;it
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;could&nbsp;be&nbsp;converted&nbsp;to&nbsp;related&nbsp;gromacs&nbsp;format.
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;Do&nbsp;you&nbsp;have&nbsp;any&nbsp;idea&nbsp;about&nbsp;this?
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;THX
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;At&nbsp;2011-05-30,"Francesco&nbsp;Oteri"<francesco.oteri>&nbsp;&nbsp;&nbsp;wrote:
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Topology&nbsp;file&nbsp;is&nbsp;suitable&nbsp;for&nbsp;analysis.&nbsp;I&nbsp;succesfully&nbsp;used&nbsp;the&nbsp;.top&nbsp;to
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;analyse&nbsp;hydrogen&nbsp;bond&nbsp;and&nbsp;salt-bridges.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;I&nbsp;don't&nbsp;know&nbsp;if&nbsp;problems&nbsp;would&nbsp;arise&nbsp;for&nbsp;simulation.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Il&nbsp;29/05/2011&nbsp;22:10,&nbsp;albert&nbsp;ha&nbsp;scritto:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much&nbsp;for&nbsp;kind&nbsp;advices.&nbsp;Here&nbsp;is&nbsp;some&nbsp;warning,&nbsp;and&nbsp;I
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;don't&nbsp;know&nbsp;whether&nbsp;there&nbsp;would&nbsp;be&nbsp;some&nbsp;problem&nbsp;or&nbsp;not:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;;&nbsp;'fake'&nbsp;gromacs&nbsp;topology&nbsp;generated&nbsp;from&nbsp;topotools.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;;&nbsp;WARNING|&nbsp;the&nbsp;purpose&nbsp;of&nbsp;this&nbsp;topology&nbsp;is&nbsp;to&nbsp;allow&nbsp;using&nbsp;the&nbsp;|WARNING
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;;&nbsp;WARNING|&nbsp;analysis&nbsp;tools&nbsp;from&nbsp;gromacs&nbsp;for&nbsp;non&nbsp;gromacs&nbsp;data.&nbsp;|WARNING
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;;&nbsp;WARNING|&nbsp;it&nbsp;cannot&nbsp;be&nbsp;used&nbsp;for&nbsp;a&nbsp;simulation.&nbsp;|WARNING
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;At&nbsp;2011-05-30,"Francesco&nbsp;Oteri"<francesco.oteri>&nbsp;&nbsp;&nbsp;&nbsp;wrote:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;Il&nbsp;29/05/2011&nbsp;21:58,&nbsp;albert&nbsp;ha&nbsp;scritto:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;Hello:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;I&nbsp;am&nbsp;wondering,&nbsp;is&nbsp;it&nbsp;possible&nbsp;to&nbsp;convert&nbsp;NAMD&nbsp;topol&nbsp;psf&nbsp;file&nbsp;into
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;Gromacs&nbsp;topol&nbsp;format?
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;Hi&nbsp;albert,
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;you&nbsp;can&nbsp;try&nbsp;with&nbsp;the&nbsp;following&nbsp;commands:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;vmd&nbsp;.psf&nbsp;.pdb
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;topo&nbsp;writegmxtop&nbsp;output.top
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;I&nbsp;recently&nbsp;tried&nbsp;with&nbsp;vmd1.9
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;--&nbsp;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>&nbsp;before&nbsp;posting!
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;Please&nbsp;don't&nbsp;post&nbsp;(un)subscribe&nbsp;requests&nbsp;to&nbsp;the&nbsp;list.&nbsp;Use&nbsp;the
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;www&nbsp;interface&nbsp;or&nbsp;send&nbsp;it&nbsp;to&nbsp;<A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;&gt;Can't&nbsp;post?&nbsp;Read&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;--&nbsp;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>&nbsp;before&nbsp;posting!
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Please&nbsp;don't&nbsp;post&nbsp;(un)subscribe&nbsp;requests&nbsp;to&nbsp;the&nbsp;list.&nbsp;Use&nbsp;the
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;www&nbsp;interface&nbsp;or&nbsp;send&nbsp;it&nbsp;to&nbsp;<A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Can't&nbsp;post?&nbsp;Read&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
&gt;&gt;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;--&nbsp;
&gt;&gt;&nbsp;&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
&gt;&gt;&nbsp;&gt;<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
&gt;&gt;&nbsp;&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>&nbsp;before&nbsp;posting!
&gt;&gt;&nbsp;&gt;Please&nbsp;don't&nbsp;post&nbsp;(un)subscribe&nbsp;requests&nbsp;to&nbsp;the&nbsp;list.&nbsp;Use&nbsp;the
&gt;&gt;&nbsp;&gt;www&nbsp;interface&nbsp;or&nbsp;send&nbsp;it&nbsp;to&nbsp;<A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.
&gt;&gt;&nbsp;&gt;Can't&nbsp;post?&nbsp;Read&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
&gt;
&gt;--&nbsp;
&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
&gt;<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>&nbsp;before&nbsp;posting!
&gt;Please&nbsp;don't&nbsp;post&nbsp;(un)subscribe&nbsp;requests&nbsp;to&nbsp;the&nbsp;list.&nbsp;Use&nbsp;the&nbsp;
&gt;www&nbsp;interface&nbsp;or&nbsp;send&nbsp;it&nbsp;to&nbsp;<A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.
&gt;Can't&nbsp;post?&nbsp;Read&nbsp;<a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
</francesco.oteri></francesco.oteri></francesco.oteri></francesco.oteri></span></pre></div></div>



</div></BLOCKQUOTE>