Hi,<div><br></div><div>depends on the tool. If the tool just need the coordinates or just velocities (dcd/vel) you don't need to convert anything because the tools can use the VMD plugins to read dcd. If the tool needs a tpr file (e.g. carges) than you need to create one. In most cases the easiest solution to do this is to use pdb2gmx. If you have a non-standard molecule for which no rtp exists you could also use psfgen+top (<a href="http://www.benlabs.net/psfgen+top/">http://www.benlabs.net/psfgen+top/</a>). </div>
<div>If the tool needs coordinates and velocities, let me know and I'll think of something.</div><div><br></div><div>Roland</div><div><br><div class="gmail_quote">On Sun, Apr 3, 2011 at 3:06 PM, Molecular Dynamics <span dir="ltr"><<a href="mailto:moleculardynamics@yahoo.com">moleculardynamics@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="margin:0cm 0cm 10pt" class="MsoNormal">
<span lang="TR"><font size="3"><font face="Calibri">Dear gmx users,</font></font></span>
</p><p style="margin:0cm 0cm 10pt" class="MsoNormal"><span lang="TR"><font size="3" face="Calibri">I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD output files. I have some NAMD output files : </font></span><tt><span style="line-height:115%;font-size:10pt">output.coor , output.vel , output.dcd </span></tt><tt><span style="line-height:115%;font-size:12pt">(binary </span></tt><font face="Calibri"><span style="line-height:115%;font-size:12pt">coordinate trajectory output file</span><tt><span style="line-height:115%;font-size:12pt">). Can I convert these output files into gromacs output files and use </span></tt><span style="line-height:115%;font-size:12pt" lang="TR">gromacs 4.5.4 analysis tools ? If it’s
possible to do it, could you please explain this job ? </span></font>
</p><p style="margin:0cm 0cm 10pt" class="MsoNormal"><span style="line-height:115%;font-size:12pt" lang="TR"><font face="Calibri">Thanks in advance</font></span><span style="line-height:115%;font-size:12pt" lang="TR">M</span></p>
<p></p><p></p></td></tr></tbody></table><br>--<br>
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