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<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>Hi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>Summary: <o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 color=blue face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;color:blue'>how</span></font></span><font
size=2 color=blue face=Verdana><span style='font-size:10.0pt;font-family:Verdana;
color:blue'> do you add timestamps to a set of <span class=SpellE>pdbs</span>
in a trajectory saved from VMD.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>Background:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>I have a concatenated set of <span
class=SpellE>pdb</span> files without any time stamps on the frames.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>I want to process them with <span
class=SpellE>g_covar</span>. However <span class=SpellE>g_covar</span> dies
immediately complaining about too <span class=GramE>many iterations</span> in <span
class=SpellE>jacobi</span>.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>I think this is because it is trying to
read the timeframe and cannot find it.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>THEREFORE: I want to add timestamps to
the frames of the trajectory.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'>I tried taking the individual frames as
PDB files and then:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=2
color=blue face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'>trjconv</span></font></span></span><font size=2 color=blue
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'> -f <span class=SpellE>X.pdb</span> -o <span class=SpellE>X.xtc</span>
-t0 1<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=2
color=blue face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'>trjconv</span></font></span></span><font size=2 color=blue
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'> -f <span class=SpellE>Y.pdb</span> -o <span class=SpellE>Y.xtc</span>
-t0 2<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=3 color=blue face=SimSun><span
style='font-size:12.0pt;color:blue'>etc</span></font></span><font color=blue><span
style='color:blue'>..<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face=SimSun><span style='font-size:
12.0pt;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=3 color=blue face=SimSun><span
style='font-size:12.0pt;color:blue'>followed</span></font></span><font
color=blue><span style='color:blue'> by <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=SpellE><span class=GramE><font size=2
color=blue face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'>trjcat</span></font></span></span><font size=2 color=blue
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'> -o <span class=SpellE>ensemble.xtc</span> *<span class=SpellE>aligned.xtc</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 color=blue face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;color:blue'>but</span></font></span><font
size=2 color=blue face=Verdana><span style='font-size:10.0pt;font-family:Verdana;
color:blue'> this failed:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:blue'>Last frame<span
style='mso-spacerun:yes'>
</span>0 time<span style='mso-spacerun:yes'> </span>1.000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:blue'>Fatal error:<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 color=blue face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:blue'>Couldn't read
time from second frame.</span></font></span><font size=2 color=blue
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;mso-bidi-font-family:"Courier New";color:blue'>Suggestions
very much appreciated<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;mso-bidi-font-family:"Courier New";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;mso-bidi-font-family:"Courier New";color:blue'>Paul<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Verdana><span style='font-size:
10.0pt;font-family:Verdana;mso-bidi-font-family:"Courier New";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>Dr Paul Barrett</span></font><font
face="Times New Roman"><span style='font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>Laboratory of
Molecular Biophysics</span></font><font face="Times New Roman"><span
style='font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>Department of
Biochemistry</span></font><font face="Times New Roman"><span style='font-family:
"Times New Roman";mso-fareast-font-family:"Times New Roman";mso-fareast-language:
EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place><st1:PlaceType><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:
yes'>University</span></font></st1:PlaceType><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:
yes'> of </span></font><st1:PlaceName><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:
yes'>Oxford</span></font></st1:PlaceName></st1:place><font
face="Times New Roman"><span style='font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:City><st1:place><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:
yes'>Oxford</span></font></st1:place></st1:City><font face="Times New Roman"><span
style='font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>OX1 3QU</span></font><font
face="Times New Roman"><span style='font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-fareast-language:EN-US;mso-no-proof:yes'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>Tel 01865 275191</span></font><font
face="Times New Roman"><span style='font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'>Fax 01865 275182</span></font><font
face="Times New Roman"><span style='font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:EN-US;mso-no-proof:yes'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
mso-fareast-language:EN-US;mso-no-proof:yes'> </span></font><font size=2
color=blue face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:blue'><o:p></o:p></span></font></p>
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