<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 10, 2010, at 4:12 PM, abdullah ahmed wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hello everyone!<span class="Apple-converted-space"> </span><br><br>I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong.<span class="Apple-converted-space"> </span><br><br>When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I get no error when I ask for COO- ):<span class="Apple-converted-space"> </span><br><br>Atom O2 not found in residue 22 while adding improper.<span class="Apple-converted-space"> </span><br><br>However, My PDB file ends with:<br>ATOM 282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00 B1 C<br>ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00 B1 O<br>ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00 B1 O<br>TER 286 LEU B 44<br><br>Therefore, the O2 atom is clearly there.<span class="Apple-converted-space"> </span><br></div></span></blockquote>in residue 44! </div><div>Would you be working with a dimer ? <br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><br>I considered the idea that the error was because there is no Hydrogen at the end of the PDB file to make the H in COOH. So I used ZZ vega to add a hydrogen to O2. When this did not work I tried adding one to O1, but I kept getting the following error:<span class="Apple-converted-space"> </span><br>"Atom H1 in residue 22 not found in rtp entry with 19 atoms..."<br><br>Thank you in advance,<br>Abdullah<br><br><hr>Hotmail: Trusted email with Microsoft’s powerful SPAM protection.<span class="Apple-converted-space"> </span><a href="https://signup.live.com/signup.aspx?id=60969" target="_new">Sign up now.</a><span class="Apple-converted-space"> </span>--<span class="Apple-converted-space"> </span><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></body></html>