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<div>Hi Justin,</div><div><font class="Apple-style-span" color="#444444" face="monospace, Verdana, Arial, sans-serif"><br></font></div><div><font class="Apple-style-span" color="#444444" face="monospace, Verdana, Arial, sans-serif"><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: Verdana; "><div style="text-indent: 0in !important; ">Thank you for your help, But when I run x2top command there is one error that is:</div><div style="text-indent: 0in !important; "><div style="text-indent: 0in !important; ">"</div><div style="text-indent: 0in !important; "><div style="text-indent: 0in !important; ">Can not find forcefield for atom C1-1 with 2 bonds</div><div style="text-indent: 0in !important; ">Can not find forcefield for atom C4-4 with 2 bonds</div><div style="text-indent: 0in !important; ">...</div></div><div style="text-indent: 0in !important; ">Program x2top, VERSION 4.0.5</div><div style="text-indent: 0in !important; ">Source code file: x2top.c, line:
207</div><div style="text-indent: 0in !important; "><br style="text-indent: 0in !important; "></div><div style="text-indent: 0in !important; ">Fatal error:</div><div style="text-indent: 0in !important; ">Could only find a forcefield type for 6 out of 24 atoms"</div><div style="text-indent: 0in !important; "><br style="text-indent: 0in !important; "></div><div style="text-indent: 0in !important; ">I don't know how can I adjust this error.</div><div style="text-indent: 0in !important; ">I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that?</div><div><br></div></div></span></font></div><span class="Apple-style-span" style="font-family: Tahoma, Verdana, Arial, sans-serif; color: rgb(68, 68, 68); "><pre style="white-space: normal; ">you zou wrote:<br>> Dear Users,<br>> <br>> I have one question about Drug-Enzyme Complex,Similar to tutorial If I <br>>
want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug <br>> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg <br>> Beta version" server too, or not?<br><br>No. You can't use two different force fields in one simulation system.<br><br>> If I can't use this server, how can I make .gro file and .itp file for <br>> drug that remove from initial .pdb file?<br>> <br><br>There are several programs in the User Contributions from the website, x2top <br>(which is distributed with Gromacs), or you can build the topology by hand. No <br>matter what you choose, you need a thorough understanding of the mechanics of <br>your chosen force field, methods of validation, and of course Chapter 5 in the <br></pre></span><div><span class="Apple-style-span" style="font-family: monospace, Verdana, Arial, sans-serif; color: rgb(68, 68, 68); ">Gromacs manual.</span></div><div><br></div><div><br><span class="App
le-style-span" style="font-family: monospace, Verdana, Arial, sans-serif; color: rgb(68, 68, 68); "></span></div><div><div>Thanks</div><div><br></div></div>
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