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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,</pre><pre style="white-space:normal">Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this is without hydrogens atoms too.</pre><pre style="white-space:normal">I think something is wrong, but I don't know what it is.In definition of "protonate" there is "<span class="Apple-style-span" style="color:rgb(0, 0, 0);font-family:Times, Verdana, Arial, sans-serif;font-size:16px"><tt style="font-family:courier, 'lucida console', serif">protonate</tt> reads (a) conformation(s) and adds all missing hydrogens as defined in <tt style="font-family:courier, 'lucida console', serif">ffgmx2.<a href="http://rocks5.vki.ac.be/gromacs/online/hdb.html" style="text-decoration:none">hdb</a></tt>." <span class="Apple-style-span" style="font-fami
ly:monospace, Verdana, Arial, sans-serif;font-size:13px;color:rgb(68, 68, 68)">but I can't add hydrogens. What is my problem?</span></span></pre><pre style="white-space:normal">Thanks</pre><pre style="white-space:normal">you zou wrote:<br>> Hi again,<br>> <br>> Sorry, I have one question now, what is the meaning of structure? I think<br>> coordinates is structure, is it true?<br>> <br><br>Yes, a coordinate file contains a structure.<br><br>> If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms<br>> are different from top file and editconf can not add hydrogens to drg.gro. If<br>> Gromacs can handle .pdb, How can it do this, because number of atoms are<br>> different(Which command I have to use?). If can't handle it how can I add<br>> Hydrogens to drg.gro?<br>> <br><br>The underlying assumption when running any simulation is that you have developed <br>the proper parameters for the ligand and that it
has an appropriate structure. <br>If you need additional hydrogens, the Gromacs "protonate" tool can generate an <br>all-atom structure.<br><br>-Justin<br><br>> Thanks,<br>> <br>> <br>> <br>> you zou wrote:<br>>> Hi again,<br>>> <br>>> Sorry I confused you with my question. My question is How can I make .gro <br>>> file and .top file from<br>> drug.pdb (that removed from drug-enzyme.pdb)?<br>>> <br>>> If I can use x2top command I will make .top file just, is it true? I think <br>>> .gro file is dependent on forcefiled too so If I use editconf command I<br>>> will miss something, is it true?<br>> <br>> If you want to use x2top, the assumption is that the structure is already <br>> appropriate as is, that is it is properly protonated. The only tool that is <br>> smart enough to add force field-specific hydrogens is pdb2gmx. If you're<br>>
using OPLS-AA, then you should have all hydrogens present, anyway. If that's<br>> true, then you can use editconf to create a .gro file (which is not<br>> absolutely necessary; Gromacs can handle .pdb files just fine). If you don't<br>> have all the appropriate atoms present in your molecule's structure, then you<br>> need to build a proper structure.<br>> <br>> -Justin<br>> <br>>> <br>>> Thank you again<br>>> <br>>> <br>>> you<br>> 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: " Can not find forcefield for atom C1-1 with 2 bonds Can not<br>>>> find forcefield for atom C4-4 with 2 bonds ...<br>>> &g t; Program x2top, VERSION 4.0.5<br>>>> Source code file: x2top.c, line: 207<br>>>> <br>>>> Fatal error: Could only find a f
orcefield type for 6 out of 24 atoms"<br>>>> <br>>> <br>>> Not all of your atom types are described by ffop
lsaa.n2t so you will have<br>>> to add them. There are only a limited number of types that are covered by <br>>> default.<br>>> <br>>> <a href="http://www.gromacs.org/Documentation/File_Formats/.n2t_File" style="font-weight:inherit;text-decoration:underline;color:rgb(0, 104, 207);cursor:pointer">http://www.gromacs.org/Documentation/File_Formats/.n2t_File</a><br>>> <br>>>> I don't know how<br>> can I adjust this error. I have one more question again,<br>>>> this command give me a top file, if I want gro file of this pdb (drug<br>>>> that has removed from drug-enzyme complex) how can I do that?<br>>>> <br>>> <br>>> Do you just need a .gro file, and not a .top? My understanding from your <br>>> first message was that you needed a topo logy. If you just need a .gro,<br>>> then simply 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<br>> one simulation system.<br>>>> <br>>>>> If I can't use this server, how can I make .gro file and .itp file for<br>>>>> <br>> & gt;>> drug that remove from initial .pdb file?<br>>>>> <br>>>> <br>>>> There are several programs in the User Contributions from the website, <br>>>> x2top (which is distributed with Gromacs), or you c
an build the topology<br>>>> by hand. No matter what you choose, you ne<br>>> ed a thorough understanding of the mechanics of<br>>>> your chosen force field, methods of validation, and of course Chapter 5<br>>>> in the<br>>>> <br>>>> Gromacs manual.<br>>>> </pre></span>
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