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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Use x2top to build your top file for the
ATP, and then used editconf to make the gro file and then u can use genbox to
put the protein and the ATP in the same box.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Btw I am not 100% on this since I have not
done it before but from the vast amounts of reading I have done this seems like
what you should do, also take a look at the manual and the wiki to find out how
to use these apps.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>~Christopher Stiles<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>College</span></font></st1:PlaceType><font
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of <st1:PlaceName w:st="on">Nanoscale</st1:PlaceName></span></font></st1:place><font
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Science and Engineering (CNSE) <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
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of <st1:PlaceName w:st="on">New York</st1:PlaceName>, <st1:place w:st="on"><st1:City
w:st="on">Albany</st1:City>, <st1:State w:st="on">New York</st1:State> <st1:PostalCode
w:st="on">12203</st1:PostalCode>, <st1:country-region w:st="on">USA</st1:country-region></st1:place></span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>mjduan@smail.hust.edu.cn<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, August 08, 2007
9:51 PM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] how to
simulate a protein and a ATP moleculesimultaneity?</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face=SimSun><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p><font size=3 face=SimSun><span style='font-size:12.0pt'>Dear GROMACS users:<br>
I want to simulate a complex composed by a protein and an ATP molecule, and
when I use the pdb2gmx to build the topology file and transfer the<strong><b><font
face=SimSun><span style='font-family:SimSun'>pdb</span></font></b></strong>
file to <strong><b><font face=SimSun><span style='font-family:SimSun'>gro</span></font></b></strong>
file, it said "<em><i><font face=SimSun><span style='font-family:SimSun'>Fatal
error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting
atoms</span></font></i></em>", So how can I build the <strong><b><font
face=SimSun><span style='font-family:SimSun'>top</span></font></b></strong>
file and <strong><b><font face=SimSun><span style='font-family:SimSun'>gro</span></font></b></strong>
file for ATP molecular and simulate the protein molcular and ATP molecule
simultaneity?<br>
Best wishes!<o:p></o:p></span></font></p>
<p><font size=3 face=SimSun><span style='font-size:12.0pt'>Mo-Jie Duan<o:p></o:p></span></font></p>
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