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>Vishal<br><br><div class="gmail_quote">On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 07/02/10 14:52, 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 All,<br>
<br>
Can anyone help me how can I go about preparing the topology file for an<br>
infinite crystal of cellulose. I have prepared the .gro file for 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 (GCLA).<br>
When I try running pdbgmx, I get an error for extra hydrogens (which is<br>
not there in itp file but is actually there in the original structure<br>
which I am using) and missing oxygen (-O).<br>
</blockquote>
<br></div>
People who might help aren't at all interested in your description of the error message. If the contents of your head were reliable, you wouldn't have seen the error in the first place, or would have solved the issue already. :-) Copy and paste your command line, and what seems to be the relevant part of the error.<br>
<br>
To use pdb2gmx, you need .rtp file entries that correspond to your monomers. If not, you will not be able to use pdb2gmx to generate your topology files.<br>
<br>
Mark<br><font color="#888888">
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</font></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>