Hi Tawhid,<br><br>The file you got was in the format used by the _program_ GROMOS. But this format is not supported by pdb2gmx/Gromacs. The GROMOS _forcefield_ is a set of equations and parameters, which stands apart from the formatting of the building blocks. You could've at least taken a bit of effort to look at the other building block definitions, and you would've seen the differences. Also, the fact that you got complaints about "#" should have been indicative to you that you were doing something wrong. In regards the building blocks (the .rtp file), read Chapter 5 (notably
5.5). This should help you to convert the GROMOS format building block to a Gromacs format one.<br><br>Tsjerk<br><br><div class="gmail_quote">On Nov 28, 2007 1:34 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">
jalemkul@vt.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">Quoting Tawhid Ezaz <<a href="mailto:ezaztaw@yahoo.com">
ezaztaw@yahoo.com</a>>:<br><br></div><div class="Ih2E3d">> I am sorry, my previous mail bounced back, as it was over 50 KB.<br>><br>> I changed the ffG43a1 to include the GTP and GDP which I got from a previous
<br>> post here. {<a href="http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html</a>}<br>><br>> I changed some structure like giving comment with ; as the origicanal # was
<br>> giving error. but now it tells me there is an error that 05* is not found in<br>> the atom type database.<br>><br>><br>><br>> Program pdb2gmx, VERSION 3.3.1<br>> Source code file: resall.c, line: 148
<br>><br>> Fatal error:<br>> Atom type O5* (residue GTP) not found in atomtype database<br>> -------------------------------------------------------<br>><br>><br>><br>> I am including the file here .the GTP residue is at the bottom of the file.
<br>><br>><br>> <a href="https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp" target="_blank">https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp</a><br>><br>> Is there any other GTP and GDP residue for the force field 43a1?
<br><br></div>Have a look at the other entries in the .rtp file, and notice how the formatting<br>of the GTP molecule you entered looks nothing like the others. Use the format<br>of other residues to guide you (paying special attention to similar molecules,
<br>like ATP, which is already a part of ffG43a1). The information in the file you<br>found appears to be in a different format, although you may still be able to<br>extract information from it.<br><br>Alternatively, you could use the PRODRG beta server to generate a
<br>suitably-formatted topology (which you can include as an .itp file in your<br>system topology). However, this topology will require editting, as some of the<br>parameters (most notably charges) will likely be unsatisfactory.
<br><font color="#888888"><br>-Justin<br></font><div><div></div><div class="Wj3C7c"><br>><br>> Thanks in advance.<br>><br>> Tawhid<br>><br>><br>><br>><br>><br>> ----- Original Message ----<br>
> From: Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Monday, November 26, 2007 9:14:37 PM
<br>> Subject: Re: [gmx-users] pdb2gmx error<br>><br>> Quoting Tawhid Ezaz <<a href="mailto:ezaztaw@yahoo.com">ezaztaw@yahoo.com</a>>:<br>><br>> > Thanks a lot Justin. It worked really nice.<br>> >
<br>> > now I am stuck with another problem. I need to add the Building block<br>> GTP and<br>> > GDP in 43a1, as I need to get the topology of a tubulin monomer. I<br>> got the<br>> > file from a old post here.
<br>> ><br>> > <a href="http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html</a><br>> ><br>> > I copied and pasted it into my file, yet, as the structure doesn't
<br>> match it<br>> > gave several errors.<br>> ><br>> > is there any way to fix this?<br>><br>> That depends entirely upon what your errors are and what you're trying<br>> to do.<br>> Please provide more details.
<br>><br>> -Justin<br>><br>> ><br>> > Thanks a lot for your help.<br>> ><br>> > Tawhid<br>> ><br>> ><br>> ><br>> > ----- Original Message ----<br>> > From: Justin A. Lemkul <
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> > To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> > Sent: Monday, November 26, 2007 7:14:43 PM
<br>> > Subject: Re: [gmx-users] pdb2gmx error<br>> ><br>> ><br>> > Quoting Tawhid Ezaz <<a href="mailto:ezaztaw@yahoo.com">ezaztaw@yahoo.com</a>>:<br>> ><br>> > > Hi,<br>> > >
<br>> > > I have just started to learn gromacs. I am facing a problem to make<br>> > topology<br>> > > file of a myoglobin. I got the pdb file from the csc tutorial.<br>> > ><br>> > > When i am running the pdb2gmx with
<br>> > ><br>> > > pdb2gmx -f conf.pdb -p topol.top<br>> > ><br>> > > i get the message, HEME148 CAB1428 0.569<br>> > > HEME148 CAC1437 0.562 0.820<br>> > > N-terminus: NH3+
<br>> > > C-terminus: COO-<br>> > > Now there are 148 residues with 1451 atoms<br>> > > -------------------------------------------------------<br>> > > Program pdb2gmx, VERSION 3.3.1<br>
> > > Source code file: pdb2top.c, line: 570<br>> > ><br>> > > Fatal error:<br>> > > atom N not found in residue 1ACE while combining tdb and rtp<br>> > > -------------------------------------------------------
<br>> > ><br>> > > I was using 43a1 force field (0), {but none of them works}.<br>> > ><br>> > > i read some previous post and got the idea that there should be a N<br>> > atom with
<br>> > > should be linked with ACE, but my conf.pdb files does not have any.<br>> I<br>> > have<br>> > > topol.top file from the tutorial but didn't show how I can generate<br>> > that.
<br>> ><br>> > Use the -ter option with pdb2gmx, and select 'none' when prompted.<br>> > That way,<br>> > pdb2gmx does not look for an N-terminal nitrogen (which is obviously<br>> > absent in
<br>> > an acetyl group).<br>> ><br>> > -Justin<br>> ><br>> > ><br>> > > I am a totally newbie, thus I am wondering what should I do. Which<br>> > file I<br>> > > should correct to get rid of those? Do I need to know the bonding
<br>> of<br>> > every<br>> > > atom in the molecule for that?<br>> > ><br>> > > Thanks in advance<br>> > ><br>> > > Tawhid<br>> > ><br>> > ><br>> > >
<br>> > ><br>> > ><br>> ><br>> ><br>> ><br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Graduate Research Assistant<br>> > Department of Biochemistry
<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>> > <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>> ><br>> > ========================================<br>> > _______________________________________________<br>> > gmx-users mailing list
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</a><br>> ><br>> ><br>> ><br>> ><br>><br>><br>><br>> ========================================<br>><br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry
<br>> Virginia Tech<br>> Blacksburg, VA<br>> <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623