Well, I also try to do this. But it seem that the atom name in my POPC pdb file (which I download from here http://terpconnect.umd.edu/~jbklauda/research/download.html ) is different from the the one in Gromacs topol database. There are 72 lips in the system in all. So, it would be very difficult to modify them one by one.<br><br>Thank you very much<br><div></div><br><pre><br>At&nbsp;2011-05-30£¬"Francesco&nbsp;Oteri"&nbsp;&lt;francesco.oteri@gmail.com&gt;&nbsp;wrote:

&gt;You&nbsp;can&nbsp;solve&nbsp;the&nbsp;problem&nbsp;without&nbsp;converting&nbsp;from&nbsp;namd&nbsp;to&nbsp;gromacs.
&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&nbsp;
&gt;topology&nbsp;through&nbsp;pdb2gmx
&gt;
&gt;Il&nbsp;29/05/2011&nbsp;22:24,&nbsp;albert&nbsp;ha&nbsp;scritto:
&gt;&gt;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much&nbsp;for&nbsp;kind&nbsp;messages.
&gt;&gt;&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&nbsp;
&gt;&gt;&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&nbsp;
&gt;&gt;&nbsp;cannot&nbsp;find&nbsp;pre-equilibrium&nbsp;CAHRMM36&nbsp;based&nbsp;POPC&nbsp;system.&nbsp;However,&nbsp;there&nbsp;
&gt;&gt;&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&nbsp;
&gt;&gt;&nbsp;could&nbsp;be&nbsp;converted&nbsp;to&nbsp;related&nbsp;gromacs&nbsp;format.
&gt;&gt;
&gt;&gt;&nbsp;Do&nbsp;you&nbsp;have&nbsp;any&nbsp;idea&nbsp;about&nbsp;this?
&gt;&gt;
&gt;&gt;&nbsp;THX
&gt;&gt;
&gt;&gt;&nbsp;At&nbsp;2011-05-30£¬"Francesco&nbsp;Oteri"&lt;francesco.oteri@gmail.com&gt;&nbsp;&nbsp;wrote:
&gt;&gt;
&gt;&gt;&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;analyse&nbsp;hydrogen&nbsp;bond&nbsp;and&nbsp;salt-bridges.
&gt;&gt;&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;&gt;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;Il&nbsp;29/05/2011&nbsp;22:10,&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;advices.&nbsp;Here&nbsp;is&nbsp;some&nbsp;warning,&nbsp;and&nbsp;I
&gt;&gt;&nbsp;&gt;&gt;&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;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;;&nbsp;'fake'&nbsp;gromacs&nbsp;topology&nbsp;generated&nbsp;from&nbsp;topotools.
&gt;&gt;&nbsp;&gt;&gt;&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;;&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;;&nbsp;WARNING|&nbsp;it&nbsp;cannot&nbsp;be&nbsp;used&nbsp;for&nbsp;a&nbsp;simulation.&nbsp;|WARNING
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;At&nbsp;2011-05-30£¬"Francesco&nbsp;Oteri"&lt;francesco.oteri@gmail.com&gt;&nbsp;&nbsp;&nbsp;wrote:
&gt;&gt;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&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;Hello:
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&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;Gromacs&nbsp;topol&nbsp;format?
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;&gt;&nbsp;&nbsp;&nbsp;Thank&nbsp;you&nbsp;very&nbsp;much
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Hi&nbsp;albert,
&gt;&gt;&nbsp;&gt;&gt;&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;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;vmd&nbsp;.psf&nbsp;.pdb
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;topo&nbsp;writegmxtop&nbsp;output.top
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;I&nbsp;recently&nbsp;tried&nbsp;with&nbsp;vmd1.9
&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;gmx-users@gromacs.org
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&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;http://www.gromacs.org/Support/Mailing_Lists/Search&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;gmx-users-request@gromacs.org.
&gt;&gt;&nbsp;&gt;&gt;&nbsp;&nbsp;&gt;Can't&nbsp;post?&nbsp;Read&nbsp;http://www.gromacs.org/Support/Mailing_Lists
&gt;&gt;&nbsp;&gt;
&gt;&gt;&nbsp;&gt;--&nbsp;
&gt;&gt;&nbsp;&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;gmx-users@gromacs.org
&gt;&gt;&nbsp;&gt;http://lists.gromacs.org/mailman/listinfo/gmx-users
&gt;&gt;&nbsp;&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;http://www.gromacs.org/Support/Mailing_Lists/Search&nbsp;before&nbsp;posting!
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&gt;
&gt;--&nbsp;
&gt;gmx-users&nbsp;mailing&nbsp;list&nbsp;&nbsp;&nbsp;&nbsp;gmx-users@gromacs.org
&gt;http://lists.gromacs.org/mailman/listinfo/gmx-users
&gt;Please&nbsp;search&nbsp;the&nbsp;archive&nbsp;at&nbsp;http://www.gromacs.org/Support/Mailing_Lists/Search&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;gmx-users-request@gromacs.org.
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</pre>