Dear Justin,<br><br>I am trying to make topology file for cellulose II. The monomer unit is glucose (residue type GLCA). I do the following:<br><br>pdb2gmx -f cellulose.gro<br><br><br>I am getting the following error while using pdbgmx.<br>
<br>"Fatal Error:<br>Atom -O not found in residue 2 while adding improper"<br><br>Atom type "O" is actually not part of the GLCA residue. Only atom type OA is part of GLCA residue. <br>Do I need to modify the rtp entry to suit my system or does this error corresponds to something else ?<br>
<br>Your help is appreciated.<br>Thanks,<br>Vishal<br><br><div class="gmail_quote">On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> 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="im"><br>
<br>
Vishal Agarwal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Mark,<br>
<br>
What I meant over here is the missing oxygen (-O) which pdbgmx complains about is not a part of .rtp entry. There is no such type of oxygen specified in any of the .atp entry of the forcefield I am using.<br>
<br>
</blockquote>
<br></div>
The "-O" is not an atom type, it indicates an oxygen atom of a previous residue. It is still not clear what it is you're doing or what the actual problem is. If you want a resolution, you'll have to do as Mark asked and post your command line and the actual error message. Remember, you're asking for free help - you have to make it easy for us to help you.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Vishal<div><div></div><div class="h5"><br>
<br>
On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 07/02/10 14:52, Vishal Agarwal wrote:<br>
<br>
Dear All,<br>
<br>
Can anyone help me how can I go about preparing the topology<br>
file for an<br>
infinite crystal of cellulose. I have prepared the .gro file for<br>
5X5X5<br>
unit cells of cellulose II using GROMACS utility and intend to apply<br>
periodic BC on it. It has a glucose molecule as building block<br>
(GCLA).<br>
When I try running pdbgmx, I get an error for extra hydrogens<br>
(which is<br>
not there in itp file but is actually there in the original<br>
structure<br>
which I am using) and missing oxygen (-O).<br>
<br>
<br>
People who might help aren't at all interested in your description<br>
of the error message. If the contents of your head were reliable,<br>
you wouldn't have seen the error in the first place, or would have<br>
solved the issue already. :-) Copy and paste your command line, and<br>
what seems to be the relevant part of the error.<br>
<br>
To use pdb2gmx, you need .rtp file entries that correspond to your<br>
monomers. If not, you will not be able to use pdb2gmx to generate<br>
your topology files.<br>
<br>
Mark<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><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<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><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>
<br>
<br>
<br>
<br>
-- <br>
Regards<br>
<br>
***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br>
---Richard Bach<br>
<br>
</div></blockquote>
<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]<a href="http://vt.edu" target="_blank">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>
========================================<div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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 www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">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>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards<br><br>***********************************************<br>Vishal Agarwal<br>Research Scholar<br>University of Massachusetts, Amherst<br>***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br> ---Richard Bach<br>