<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Dear Dr. Roland Schulz, <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt" class=yiv1358808750msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"> <o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750yiv1872873810yiv1079269607msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Thank you very much for your attention. I have Amber type ff <SPAN style="mso-spacerun: yes"> </SPAN>that includes bond, angle, dihedral and nonbounded interaction terms in Charmm file format. Should I use the patch to generate a gromacs topology from psf file ? <o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; COLOR: black; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; COLOR: black; FONT-SIZE: 11pt">I have NAMD created.coor and .vel files that have the final coordinates and velocities. Also I have a dcd trajectory file. And according to these informations what is the next step after getting the gromacs topology file to <SPAN style="mso-spacerun: yes"> </SPAN></SPAN><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">continue a NAMD simulation in Gromacs ? What should I do ? <o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1358808750yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Kind regards.<o:p></o:p></SPAN></DIV><BR><BR>--- On <B>Thu, 9/30/10, Roland Schulz <I><roland@utk.edu></I></B> wrote:<BR>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>From: Roland Schulz <roland@utk.edu><BR>Subject: Re: NAMD simulation in Gromacs<BR>To: "oguz gurbulak" <gurbulakoguz@yahoo.com>, "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Thursday, September 30, 2010, 6:28 PM<BR><BR>
<DIV id=yiv658546532>Oguz,<BR><BR>
<DIV class=yiv658546532gmail_quote>On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <SPAN dir=ltr><<A href="http://us.mc363.mail.yahoo.com/mc/compose?to=gurbulakoguz@yahoo.com" rel=nofollow target=_blank ymailto="mailto:gurbulakoguz@yahoo.com">gurbulakoguz@yahoo.com</A>></SPAN> wrote:<BR>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv658546532MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Dear Dr. Roland Schulz, </SPAN></DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; COLOR: black; FONT-SIZE: 11pt">Thank you very much for your attention. I would like to have a copy of patch that generates gromacs topology from psf file. And could you please explain how to use this patch in detail ? Because I have no information on Pär's scripts.</SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
<DIV>Do you have standard CHARMM or Amber FF? Than you don't need to convert the FF because it is already part of GROMACS. </DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">I think, In order to continue a NAMD simulation in Gromacs I should first save the last coordinates (.coor file in namd ) as a pdb file and convert it into gro file . But there are many ways to get a gro file</SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
<DIV>no you don't need to convert the coordinate file or get the last frame. </DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">- using pdb2gmx ( but I should choose the force field in gromacs. This may be a problem. ) By the way, I changed CHARMM force field and use Amber type force field in NAMD.</SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
<DIV>Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a standard molecule (e.g. protein), it will be much easier to just use pdb2gmx to generate the topology.</DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Could you share your ideas about this process ? What should I do ?</SPAN><SPAN style="FONT-SIZE: small" class=yiv658546532Apple-style-span> </SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
<DIV>You would just do everything the same way as setting up a new simulation and use the last frame as starting structure. Make sure you use a structure which includes both coordinates and velocities. </DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"></SPAN><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><SPAN> </SPAN>Is there a way to get a tpr file from NAMD files? </SPAN> </DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
<DIV>No. Not automatically. You need to get all the input files (grompp.mdp, topol.top, conf.gro) and then run grompp to generate your tpr.</DIV>
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<DIV>Roland </DIV>
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<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Kind regards.</SPAN> </DIV>
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<P style="MARGIN: 0cm 0cm 0pt"><SPAN><SPAN style="FONT-SIZE: 10.5pt">Oguz</SPAN></SPAN><SPAN style="FONT-SIZE: 10.5pt"> GURBULAK Ph.D. Student<BR>Ege University - Faculty of Science<BR><SPAN>Department of Physics </SPAN><BR>Branch of Atomic and <SPAN>Molecular Physics</SPAN></SPAN> </DIV>
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<DIV></DIV></TD></TR></TBODY></TABLE><BR></BLOCKQUOTE></DIV><BR><BR clear=all><BR>-- <BR>ORNL/UT Center for Molecular Biophysics <A href="http://cmb.ornl.gov/" rel=nofollow target=_blank>cmb.ornl.gov</A><BR>865-241-1537, ORNL PO BOX 2008 MS6309<BR></DIV></BLOCKQUOTE></td></tr></table><br>