<div>Let me clarify.</div>
<div> </div>
<div>I have no problem determining the bond stretching or angle bending parameters for HCN. This was a very straightforward task. Unit conversion to get those values in a gromacs force field was also a non-issue.</div>
<div> </div>
<div>The problems I am having are:</div>
<div> </div>
<div>1) How do I specify a POLAR hydrogen on a carbon atom? There are polar hydrogens (or so it seems) in the gromacs forcei field, but ostensibly they are on heteroatoms such as nitrogen or oxyen. Is there a way to force gromacs to let a polar hydrogen on a carbon?</div>
<div> </div>
<div>2) I AM looking for advice on the van der Waals parameters. Yes, I can guess and tweak until the cows come home, but obviously there are recommendations which I do not know. So... any suggestions on this.</div>
<div> </div>
<div>3) The problem is quite simple, I want to develop parameters for HCN so I can use it as both ligand AND as a component n a solvent box. I do have the formula (4 or 5 steps from the web) to create my solvent box, but I need to have HCN properly parameterized. </div>
<div> </div>
<div>4) I am asking for this as I cannot use the Dundee server to make the appropriate topology file.</div>
<div> </div>
<div>The warning blurb was good at saying "Parameter development is done by professionals, so please do not try this at home." I am asking for help in the above issues as I am new to GROMACS but NOT other MD programs.</div>
<div> </div>
<div>Thanks again for any help. </div>
<div><br><br> </div>
<div class="gmail_quote">On Thu, Jun 3, 2010 at 7:30 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>----- Original Message -----<br>From: Mark Zottola <<a href="mailto:mzottola@gmail.com" target="_blank">mzottola@gmail.com</a>><br>Date: Friday, June 4, 2010 1:55<br>Subject: [gmx-users] Creation of a Non-Standard Residue<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br>
<div><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font>I am trying to to create a non-standard residue - HCN. This cannot be done by the Dundee PRODRG server as it subsumes the polar hydrogen into the carbon. This results in a diatomic molecule that the program cannot handle.</div>
<div><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font> </div> </div>
<div>
<div class="im"><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font>I do mind creating a new drug by hand, but a search through the email list has been less than fruitful. I have done parameter/non-standard residue formation in AMBER, I believe I understand the process. Yet, there is no clear delineation of how one does charges. The best I found was the proper suggestion that CHELPG charges from a QM calculation should be employed. This is to be expected, but WHICH method should one use: hf/6-31g*, MNDO, something else?<br>
<br></div>The standard advice is here <a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a>. For starters, choose a force field you want to parameterize HCN to work *with*.<br>
</div>
<div><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal"> </font> <br></div>
<div>
<div class="im"><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font>I know I will have to augment my parameter file to include the new atom types and parameters. But as HCN has a polar hydrogen "on a carbon" how do I ensure that this is explicitly maintained? If I lie and call the hydrogen on carbon "H", the designation for an atom bonded to Nitrogen, is this enough to keep that hydrogen explicit? I also want to make a solvent box of HCN (cheaper and safer than trying this experimentally!!). I am assuming that simple electrostatics balanced against Van der Waals interactions will dictate the proximity of hydrogen bond donor to acceptor in this forcefield. <br>
<br></div>You seem to be creating problems for yourself by not having a clear objective - or at least not expressing it here!<br></div>
<div> <br></div>
<div>
<div class="im"><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font>Finally, I assume a kluge of non-bonded parameters (van derWaals) is reasonable or is there a preferred way of determining an L-J potential?<br>
<br></div>Guessing values randomly is likely to get random results. Parameterization and validation of parameters are difficult topics to work on, and not encouraged for newcomers.<br></div>
<div>
<div></div>
<div class="h5">
<div> <br></div>
<div><font style="BACKGROUND-COLOR: rgb(245,248,240); FONT-STYLE: normal; FONT-SIZE: 14px; FONT-WEIGHT: normal">> </font>If I totally missed the answers to these questions, a hint on better keywords or a good reference encompassing these issues would be welcome.</div>
<br></div></div><font color="#888888">Mark </font><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>