Dear Justin,<br><br>Thanks for replying.<br><br><div class="gmail_quote"><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"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
pdb2gmx -f cellulose.gro<br>
<br>
</blockquote>
<br></div>
So then your "cellulose.gro" contains all the atoms of GLCA monomers, named exactly as the force field expects them? Have you checked against the .rtp entry? What force field are you using?<div class="im"><br>
;;<br></div></blockquote><div>Should they be exactly in the same order as the rtp entry ? The atom type I specified is definitely according to the standard convention of rtp entry. I am using G45a3 as the force field.<br>
<br></div><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">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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>
</blockquote>
<br></div>
pdb2gmx is complaining about an atom, not an atom type. Somewhere in the .rtp file (probably within the [impropers] section, there should be a line specifying an atom named O that belongs to the preceding residue (hence the minus sign). None of my .rtp files are like this. Did you create a custom .rtp entry?<div class="im">
<br></div></blockquote><div>;; <br></div><div>No I didnt create a custom rtp entry. <br></div><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>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Do I need to modify the rtp entry to suit my system or does this error corresponds to something else ?<br>
<br>
</blockquote>
<br></div>
That will depend upon the answers to the above questions. If you created the .rtp entry, then you'll have to fix the problem of naming mismatch. If you're using the standard .rtp entry for the force field, then it's easier to modify your coordinate file to match the naming expected by the force field.<br>
<br></blockquote><div>;;<br>The problem I am having is where to modify my coordinate file. The residue doesnot contain a atom type 'O'. <br><br>Another curious question I have is suppose if I have another system where the a monomer uint say GLCA (specified in rtp) is connected by a bridging atom say Carbon. Do I need to create a new rtp entry for pdbgmx to work or is there a work around by specifying that carbon as a separate residue ?<br>
<br><br>Again thanks for replying.<br><br>Best,<br>Vishal<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-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;"><div class="im">
Your help is appreciated.<br>
Thanks,<br>
Vishal<br>
<br></div><div><div></div><div class="h5">
On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Vishal Agarwal wrote:<br>
<br>
Dear Mark,<br>
<br>
What I meant over here is the missing oxygen (-O) which pdbgmx<br>
complains about is not a part of .rtp entry. There is no such<br>
type of oxygen specified in any of the .atp entry of the<br>
forcefield I am using.<br>
<br>
<br>
The "-O" is not an atom type, it indicates an oxygen atom of a<br>
previous residue. It is still not clear what it is you're doing or<br>
what the actual problem is. If you want a resolution, you'll have to<br>
do as Mark asked and post your command line and the actual error<br>
message. Remember, you're asking for free help - you have to make<br>
it easy for us to help you.<br>
<br>
-Justin<br>
<br>
Vishal<br>
<br>
<br>
On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham<br>
<<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>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<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<br>
file for<br>
5X5X5<br>
unit cells of cellulose II using GROMACS utility and<br>
intend to apply<br>
periodic BC on it. It has a glucose molecule as building<br>
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<br>
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<br>
have<br>
solved the issue already. :-) Copy and paste your command<br>
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<br>
your<br>
monomers. If not, you will not be able to use pdb2gmx to generate<br>
your topology files.<br>
<br>
Mark<br>
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-- 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>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div class="h5"><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>
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<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>
</div></div></blockquote><div><div></div><div class="h5">
<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>
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</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>