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<span class="Apple-style-span" style="font-family:Tahoma, Verdana, Arial, sans-serif;color:rgb(68, 68, 68)"><pre style="white-space:normal">Hi again, </pre><pre style="white-space:normal">Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? </pre><pre style="white-space:normal">If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true?</pre><pre style="white-space:normal">Thank you again</pre><pre style="white-space:normal"><br></pre><pre style="white-space:normal">you zou wrote:<br>> Hi Justin,<br>> <br>> Thank you for your help, But when I run x2top command there is one error <br>> that is:<br>> "<br>> Can not find forcefield for atom C1-1 with 2 bonds<br>> Can not find forcefield for atom C4-4 with 2 bonds<br>> ...<br>&g
t; Program x2top, VERSION 4.0.5<br>> Source code file: x2top.c, line: 207<br>> <br>> Fatal error:<br>> Could only find a forcefield type for 6 out of 24 atoms"<br>> <br><br>Not all of your atom types are described by ffoplsaa.n2t so you will have to add <br>them. There are only a limited number of types that are covered by default.<br><br><a href="http://www.gromacs.org/Documentation/File_Formats/.n2t_File" style="font-weight:inherit;text-decoration:none;color:rgb(0, 104, 207);cursor:pointer">http://www.gromacs.org/Documentation/File_Formats/.n2t_File</a><br><br>> I don't know how can I adjust this error.<br>> I have one more question again, this command give me a top file, if I <br>> want gro file of this pdb (drug that has removed from drug-enzyme <br>> complex) how can I do that?<br>> <br><br>Do you just need a .gro file, and not a .top? My understanding from your first <br>message was that you needed a topo
logy. If you just need a .gro, then simply <br>pass your .pdb file to editconf.<br><br>-Justin<br><br>> you zou wrote:<br>>> Dear Users,<br>>> <br>>> I have one question about Drug-Enzyme Complex,Similar to tutorial If I <br>>><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 ne
ed a thorough understanding of the mechanics of <br>> your chosen force field, methods of validation, and of course Chapter 5 in the <br>> <br>> Gromacs manual.<br>> <br></pre></span>
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