Hi David,<br>I could figure out that parameters for NAG are not that important. So, I deleted them and used pdb2gmx to get the topology.<br>I started running it, but I realize that the protein started to rotate around the center of mass with a frequency of around 200ps.
<br>I used "Linear" as an option for comm_mode and I used "Protein" in comm_grps.<br>Any reason Why the protein is rotating around its center of mass, is it normal?<br>Thanks in advance.<br>-Vissu.<br>
<br><div><span class="gmail_quote">On 8/8/06, <b class="gmail_sendername">David Mobley</b> <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Vissu,<br><br>Depends on what you are trying to do. Many proteins deposited in the<br>pdb contain "uninteresting" ligands bound to them (i.e. cosolvent<br>molecules, etc.) On the other hand, sometimes ligands are functionally
<br>important or significantly affect the structure. You have to decide<br>whether you want to include NAG or not; it might help to first figure<br>out what it is and what it's used for (perhaps look up its name, and<br>look at the paper and PDB headers...).
<br><br>It is obviously harder to come up with parameters for NAG than not. If<br>you end up deciding it's not important, you can, for example, just<br>remove the HETATM entries dealing with it before running pdb2gmx.<br>
<br>David<br><br><br>On 8/7/06, Viswanadham Sridhara <<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a>> wrote:<br>> Hi Everyone,<br>> I am trying to simulate a protein and I am getting the following error
<br>> message.<br>> "NAG" not found in residue topology database. I checked gmx-users discussion<br>> list to find out if someone ever used 1HEW.pdb . Its a hen egg-white<br>> lysozyme. I did not get even a single archive about this.
<br>> It is under HETATM section of .pdb file. Any help is appreciated.<br>> I know that I have to add this residue in aminoacids.dat file and create<br>> atoms and bonds in .rtp section. Is there any other way around?
<br>> Thanks in advance,<br>> -Vissu<br>><br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University,<br>> Norfolk, VA-23529.<br>> _______________________________________________
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</div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Research Assistant,<br>Old Dominion University,<br>Norfolk, Va-23529.