<pre><tt><tt>Dear users,<br> I tried the prodrg beta version as well, but i still dont understand, it does consider <br>the aromatic hydrogens but deletes the polar hydrogens on the H2PO3- groups.<br>I am adding the pdb file under please do help if you can. <br><br></tt></tt><tt><tt></tt></tt>ATOM 1 C1 FNP X 301 43.226 14.934 14.797 1.00 44.35 C<br>ATOM 2 C2 FNP X 301 44.293 10.378 18.585 1.00 46.18 C<br>ATOM 3 C3 FNP X 301 43.672 9.449 17.765 1.00 45.78 C<br>ATOM 4 C4 FNP X 301 43.020 9.807 16.600 1.00 46.76 C<br>ATOM 5 C5 FNP X 301 42.973 11.154 16.208 1.00 44.76 C<br>ATOM 6 C6 FNP X 301 42.316 11.539 15.028 1.00 45.10 C<br>ATOM 7 C7 FNP X 301 42.279 12.860 14.658 1.00 40.66 C<br>ATOM 8 C8 FNP X 301 42.872 13.827 15.410 1.00 43.25 C<br>ATOM 9 C9 FNP X 301
43.543 13.479 16.610 1.00 42.55 C<br>ATOM 10 C10 FNP X 301 43.595 12.136 17.015 1.00 42.79 C<br>ATOM 11 C11 FNP X 301 44.247 11.734 18.197 1.00 44.68 C<br>ATOM 12 C12 FNP X 301 44.591 10.019 19.824 1.00 47.63 C<br>ATOM 13 F1 FNP X 301 43.227 16.081 15.714 1.00 50.37 F<br>ATOM 14 F2 FNP X 301 44.408 14.813 14.265 1.00 49.42 F<br>ATOM 15 P1 FNP X 301 42.067 15.861 13.661 1.00 44.69 P<br>ATOM 16 OP1 FNP X 301 40.877 15.050 13.339 1.00 39.80 O<br>ATOM 17 OP2 FNP X 301 42.755 16.211 12.386 1.00 36.98 O<br>ATOM 18 OP3 FNP X 301 41.592 17.133 14.280 1.00 41.94 O<br>ATOM 19 F3 FNP X 301 43.581 9.096 20.394 1.00 48.34 F<br>ATOM 20 F4 FNP X 301 44.725 11.047 20.617 1.00 48.68 F<br>ATOM 21 P2 FNP X 301
45.850 8.709 20.178 1.00 48.40 P<br>ATOM 22 OP4 FNP X 301 45.680 7.563 19.249 1.00 46.60 O<br>ATOM 23 OP5 FNP X 301 45.707 8.197 21.564 1.00 48.03 O<br>ATOM 24 OP6 FNP X 301 47.227 9.248 20.030 1.00 44.37 O<br>ATOM 25 H3 FNP X 301 43.699 8.397 18.049 1.00 0.00 H<br>ATOM 26 H4 FNP X 301 42.542 9.044 15.986 1.00 0.00 H<br>ATOM 27 H6 FNP X 301 41.834 10.786 14.404 1.00 0.00 H<br>ATOM 28 H7 FNP X 301 41.763 13.141 13.740 1.00 0.00 H<br>ATOM 29 H9 FNP X 301 44.017 14.252 17.216 1.00 0.00 H<br>ATOM 30 H11 FNP X 301 44.726 12.486 18.825 1.00 0.00 H<br>ATOM 31 HP2 FNP X 301 43.142 17.163 12.454 1.00 0.00 H<br>ATOM 32 HP3 FNP X 301 42.310 17.862 14.162 1.00 0.00 H<br>ATOM 33 HP4 FNP X 301
44.891 7.750 18.613 1.00 0.00 H<br>ATOM 34 HP6 FNP X 301 47.898 8.604 20.473 1.00 0.00 H<br>END<br><br><tt><tt><br>Message: 2<br>Date: Thu, 10 Jan 2008 07:18:39 -0500<br>From: "Justin A. Lemkul" <<span style="border-bottom: 1px dashed rgb(0, 102, 204); background: transparent none repeat scroll 0% 50%; cursor: pointer; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;" class="yshortcuts" id="lw_1200329357_14">jalemkul@vt.edu</span>><br>Subject: Re: [gmx-users] Generating topology file for a molecule (FNP)<br> not in the gromacs library.<br>To: Discussion list for GROMACS users <<span style="border-bottom: 1px dashed rgb(0, 102, 204); background: transparent none repeat scroll 0% 50%; cursor: pointer; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;" class="yshortcuts"
id="lw_1200329357_15">gmx-users@gromacs.org</span>><br>Message-ID: <<span style="border-bottom: 1px dashed rgb(0, 102, 204); background: transparent none repeat scroll 0% 50%; cursor: pointer; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;" class="yshortcuts" id="lw_1200329357_16">1199967519.47860d1fe290a@webmail.vt.edu</span>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>Quoting Mufaddal Soni <muffi_gro@yahoo.com>:<br><br>> Dear users,<br>> I am working with PTP1B protein. Recently I tried to<br> run it<br>> in gromacs along with an inhibitor<br>> {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-<br> 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC<br>> ACID [FNP in short]. The problem is that gromacs does not<br> recognize FNP<br>> and hence I am not able to generate a topology file of it using<br> pdb2gmx. I<br>> tried using the The Dundee PRODRG server
to generate the topology<br> file with<br>> the pdb file as the input. The problem is that it does generate the<br> topology<br>> file but without any hydrogens. Even the polar hydrogens information<br> is not<br>> available inspite of it being a part of my input pdb file. Thus I am<br> not able<br>> to use FNP with the polar hydrogens for my runs.<br>><br>> If anyone has faced similar problems please do help if you can.<br><br>I know that PRODRG (which I believe uses the old ffgmx) does not add<br> aromatic<br>hydrogens to molecules, but the PRODRG beta site (which uses GROMOS96)<br> does. <br>You may want to try the beta server, since ffgmx is deprecated (as<br> noted in the<br>manual).<br><br>-Justin<br><br>><br>> Thanking you,<br>> Cheers.<br>><br>> Soni Mufaddal Saifee,<br>> B.Tech IIT Madras.<br>><br>><br>> ---------------------------------<br>> Be a better friend, newshound, and know-it-all with <span
style="border-bottom: 1px dashed rgb(0, 102, 204); background: transparent none repeat scroll 0% 50%; cursor: pointer; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;" class="yshortcuts" id="lw_1200329357_17">Yahoo! Mobile</span>.<br> Try it<br>> now.<br><br><br><br></tt></tt></pre><p> 
<hr size=1>Never miss a thing. <a href="http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs"> Make Yahoo your homepage.</a>