Dear gromacs users,<br><br>I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving unreliable output, I generated Amber topology and
coordinate files for GTP molecule. Then, I converted them into the
corresponding gromacs topology (.top) and coordinate files (.gro) and generated parameter (.itp) file using following command (Thanks to <span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial,sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; background-color: rgba(255, 255, 255, 0.918); display: inline ! important; float: none;">Tsjerk)</span>:<br>
<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial,sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; background-color: rgba(255, 255, 255, 0.918); display: inline ! important; float: none;">sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e '/^\s*\[\s*moleculetype\s*\]\</span><span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial,sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; background-color: rgba(255, 255, 255, 0.918); display: inline ! important; float: none;">s*$/,$p' TOP > ITP</span><br>
<br>But the topology and co-ordinates file are quite different from the input PDB file and hence the parameters are also faulty, the GDP molecule is not fitting in the binding pocket of protein. Upon tracking the whole process, it was found that the error might be while using antechamber for generating prepin file using Gaussian output file as the input. <br>
<br>Can anyone please suggest some way to apply some constraints in the antechamber command itself. OR if anybody has the paramters or topology for GDP, can anyone provide me the same so that I can compare and see where the parameters are differing.<br>
<br>Thanks<br clear="all"><br><font style="font-family: trebuchet ms,sans-serif;" size="2">----<br>Neeru Sharma<br></font><font style="font-family: trebuchet ms,sans-serif;" size="2">Pune (India)</font>