<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><p style="margin-bottom: 0cm;">Dear All,</p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;">I'm trying to create gro and .top files
using <font face="Times New Roman, serif"><font size="3">pdb2gmx. I
created n-dodecane.pdb using Chem3D and got 100 molecules using
packmol. I added TER cards between each seperate molecules. Then I tried to get gro
and .top files using the commands in below :</font></font></p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;"><font face="Times New Roman, serif"><font size="3">pdb2gmx
–ff G43a2</font></font><font face="Times New Roman, serif"><font size="3">
</font></font><font face="Times New Roman, serif"><font size="3">–f
n-dodecane.pdb –o n-dodecane.gro –p n-dodecane.top</font></font></p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;"><font face="Times New Roman, serif"><font size="3">pdb2gmx
–ff G43a2</font></font><font face="Times New Roman, serif"><font size="3">
</font></font><font face="Times New Roman, serif"><font size="3">–f
n-dodecane.packmol100.pdb –o n-dodecane.gro –p n-dodecane.top (
added TER cards )</font></font></p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;"><font face="Times New Roman, serif"><font size="3">pdb2gmx
–ff G43a2</font></font><font face="Times New Roman, serif"><font size="3">
</font></font><font face="Times New Roman, serif"><font size="3">–f
n-dodecane.packmol100.pdb –o n-dodecane.gro –p n-dodecane.top</font></font></p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;"><font face="Times New Roman, serif"><font size="3">I
couldn't get gro and .top files. Could you please help me to get
gro and .top files successfuly ? I also need some information about
using packmol <span style="border-bottom: 1px dashed rgb(0, 102, 204); cursor: pointer;" class="yshortcuts" id="lw_1236362656_0">pdb file</span> in Gromacs. I want to run md for 100
n-dodecane molecules. </font></font>
</p>
<p style="margin-bottom: 0cm;"><br>
</p>
<p><font face="Times New Roman, serif"><font size="3"><font face="Times New Roman, serif">Thank
you very much for your attention.</font></font></font></p>
<p style="margin-bottom: 0.35cm; line-height: 115%;"><br><br>
</p>
<p style="margin-bottom: 0.35cm; line-height: 115%;"><font face="Times New Roman, serif"><font size="3">Sincerely</font></font></p></td></tr></table><br>