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The gromacs version is 3.3.1, which I am using on cygwin in the windows enviroment. <br>The command I used is: "pdb2gmx -f test.pdb -p test.top -o test.gro -ter"<br>and the forcefield is Encad all- atom forcefield, using scaled down vacuum charges. <br><br>> Date: Mon, 10 May 2010 11:00:06 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] naive question about the c-terminus<br>> <br>> <br>> <br>> abdullah ahmed wrote:<br>> > I'm sorry I should have been more clear. Because the PDB file starts <br>> > from residue number 23, the residue labelled 44 in the PDB is the <br>> > residue that the error message refers to. Actually there is no residue <br>> > 22 in the PDB file.<br>> > <br>> > You are also somewhat correct in saying that there are more than one <br>> > chains. Currectly I am working on one chain, but the original structure <br>> > I was working on had 10 chains (from A -J). This is why it is labelled <br>> > "B". <br>> > <br>> <br>> Then we'll need a lot more information: Gromacs version, your *exact* command <br>> line, and what force field you're using, at least. The .pdb file should work <br>> fine with O1 and O2; the .tdb file should rename them to O and OT, when adding <br>> the hydrogen (HO), so I don't know why O2 is staying in place when impropers are <br>> being added.<br>> <br>> -Justin<br>> <br>> > > Date: Mon, 10 May 2010 10:29:18 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] naive question about the c-terminus<br>> > ><br>> > ><br>> > ><br>> > > abdullah ahmed wrote:<br>> > > > Hello everyone!<br>> > > ><br>> > > > I have a naive question and I have been trying to find a solution<br>> > > > myself, but I just don't understand what is wrong.<br>> > > ><br>> > > > When I run pdb2gmx with "-ter" on my molecule I get the following <br>> > error<br>> > > > message when I ask for a COOH to be made at the C terminus (I get no<br>> > > > error when I ask for COO- ):<br>> > > ><br>> > > > Atom O2 not found in residue 22 while adding improper.<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<br>> > > > B1 C<br>> > > > ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00<br>> > > > B1 O<br>> > > > ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00<br>> > > > B1 O<br>> > > > TER 286 LEU B 44<br>> > > ><br>> > > > Therefore, the O2 atom is clearly there.<br>> > > ><br>> > ><br>> > > The error message comes from residue 22, not 44. I'm guessing there <br>> > is another<br>> > > chain, for which residue 22 is the C-terminus? Likely this one is <br>> > missing O2.<br>> > ><br>> > > > I considered the idea that the error was because there is no <br>> > Hydrogen at<br>> > > > the end of the PDB file to make the H in COOH. So I used ZZ vega to <br>> > add<br>> > > > a hydrogen to O2. When this did not work I tried adding one to O1, <br>> > but I<br>> > > > kept getting the following error:<br>> > > > "Atom H1 in residue 22 not found in rtp entry with 19 atoms..."<br>> > > ><br>> > ><br>> > > The force field expects that all of the atoms in the residue have <br>> > specific<br>> > > names. Adding a hydrogen should be done automatically, from the .hdb <br>> > and/or<br>> > > .tdb file(s).<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Thank you in advance,<br>> > > > Abdullah<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign<br>> > > > up now. <https://signup.live.com/signup.aspx?id=60969><br>> > > ><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > MILES-IGERT Trainee<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > --<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > ------------------------------------------------------------------------<br>> > Hotmail: Powerful Free email with security by Microsoft. Get it now. <br>> > <https://signup.live.com/signup.aspx?id=60969><br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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