<br>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">Dear All,</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">I have created Amber input file (.prmtop and .rst7)
using Xleap. And then I have converted this input file into Gromacs input file
format (*.gro and *.top) with <a href="http://amb2gmx.pl/" target="_blank"><span style="color:blue">amb2gmx.pl</span></a> script. I did simulation using Gromacs
Package (Amber Force Field). Now I would like to convert Gromacs trajectory
file to Amber trajectory file format. So that I can easily analyses this
trajectory. I tried to convert Gromacs (.xtc) trajectory file to Amber (.mdcrd)
trajectory file using VMD. This VMD converted trajectory is not working fine
for DCCM (Dynamic cross correlation Matrix) analysis. </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">Now i'm trying to convert Gromacs trajectory into dcd format, and then
use ptraj to read the dcd file and write the mdcrd (or AMBER netcdf)
trajectory. </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">Example:</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">-----------</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN"> [1] Gromacs20ns.xtc </span><span style="mso-bidi-font-size:12.0pt;
line-height:150%;font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-IN;mso-char-type:
symbol;mso-symbol-font-family:Wingdings"><span style="mso-char-type:symbol;
mso-symbol-font-family:Wingdings">à</span></span><span style="mso-bidi-font-size:
12.0pt;line-height:150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-IN"> nojump.xtc (using
trjcat/trjconv)</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">[2] nojump.xtc </span><span style="mso-bidi-font-size:12.0pt;line-height:
150%;font-family:Wingdings;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-IN">à</span><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-IN">
amber20ns.dcd (using VMD)</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">[3] Ptraj file conversion </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajin amber20ns.dcd</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajout <a href="http://amber20ns.nc/" target="_blank"><span style="color:blue">amber20ns.nc</span></a> netcdf</span></p>
<p class="MsoNormal" style="margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt;line-height:150%;
text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:150%;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">(or)</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">Is it necessary to do image for this file.</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajin test.dcd</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">center origin</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">image origin center </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajout <a href="http://amber20ns.nc/" target="_blank"><span style="color:blue">amber20ns.nc</span></a> netcdf</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">Is this correct procedure?</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">I want to do DCCM (Dynamic cross correlation
analysis). </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">DCCM Ptraj file</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">----------------</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajin test.rst7</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">trajin <a href="http://amber20ns.nc/" target="_blank"><span style="color:blue">amber20ns.nc</span></a></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">strip :WAT</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">strip :Cl-</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">center :1-85 origin</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">image origin center</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">matrix correl name corr @CA out amber20ns.dccm byres</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN">If you have any ptraj file format for this.</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%;text-autospace:none"><span style="mso-bidi-font-size:12.0pt;line-height:
150%;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
mso-fareast-language:EN-IN"> Actually i did simulation based on NPT
ensemble. Is it necessary to mention the BOX dimensions in any were in the dcd
file creation?</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN">Already i tried to convert Gromacs trajectory into PDB (total
trajectory) but it is not working well for the analysis purpose of AMBER.</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"><span style="mso-bidi-font-size:12.0pt;line-height:150%;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman";mso-fareast-language:
EN-IN"><br>
Eagerly waiting for your suggestion<br>
<br>
Regards<br>
Raja</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
150%"> </p>
<br><div class="gmail_quote">On Fri, Jun 17, 2011 at 6:46 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<u></u>
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 17/06/2011 2:57 AM, Raja Pandian wrote:
<blockquote type="cite"><br>
<div class="gmail_quote"><br>
<p class="MsoNormal" style="text-align:justify">Dear All,</p>
<p class="MsoNormal" style="text-align:justify">I have created
Amber input file (.prmtop
and .rst7) using Xleap. And then I have converted this input
file into Gromacs
input file format (*.gro and *.top) with <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> script. I did simulation
using Gromacs Package (Amber Force Field). Now I would like to
convert Gromacs
trajectory file to Amber trajectory file format. So that I can
easily analyses this
trajectory. I tried to convert Gromacs trajectory file to
Amber trajectory file
using VMD. This VMD converted trajectory is not working fine.
Pls help me in
this regards</p>
</div>
</blockquote>
<br></div>
You really haven't said what you've done at the critical point, nor
why you think it is not working. So we are unable to help at this
time.<br>
<br>
Maek<br>
</div>
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