Oguz,<br><br><div class="gmail_quote">On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <span dir="ltr"><<a href="mailto:gurbulakoguz@yahoo.com">gurbulakoguz@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit"><p style="text-align:justify;margin:0cm 0cm 0pt" class="MsoNormal"><span style="font-family:Arial;font-size:11pt">Dear Dr. Roland Schulz, </span>
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</p><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></p>
</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><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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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></p>
</td></tr></tbody></table></blockquote><div>no you don't need to convert the coordinate file or get the last frame. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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</p><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></p>
</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>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit"><p style="text-align:justify;margin:0cm 0cm 0pt">
<font class="Apple-style-span" face="Arial" size="7"><span class="Apple-style-span" style="font-size: 25px;"><br></span></font></p><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 class="Apple-style-span" style="font-size: small; "> </span></p>
</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><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> </p>
</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><div><br></div><div>Roland </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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</p><p style="text-align:justify;margin:0cm 0cm 0pt"><span style="font-family:Arial;font-size:11pt">Kind regards.</span>
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</p><p style="margin:0cm 0cm 0pt"><span><span style="font-family:'Courier New';font-size:10.5pt">Oguz</span></span><span style="font-family:'Courier New';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>
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</blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>