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On 9/02/2011 4:56 PM, bipin singh wrote:
<blockquote
cite="mid:AANLkTinBYW=i1iAOn8sDGcBfjuxv=W8y=QrZukjXUvo7@mail.gmail.com"
type="cite">Sir,<br>
Actually ARG is present as a ligand bound to RNA molecule....<br>
</blockquote>
<br>
Then you've got work to do. pdb2gmx copes well with linear polymers
of predefined monomers, which you don't have. You will need to
become very conversant with chapter 5 of the manual. Various how-tos
on the wiki will help too.<br>
<br>
One solution is to generate a topology for base-bound-to-arginine by
hand based on the building blocks in the respective .rtp files.
Check that topology is useful for vacuum MD of that hybrid residue.
Then modify it to be a new .rtp entry, update the forcefield
database accordingly. Only then can pdb2gmx deal with it.<br>
<br>
Another is to use AMBER's leap module to generate a topology for
base-bound-to-arginine, and convert the topology representation
somehow (IIRC there might be a tool for that). Then proceed as
above.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinBYW=i1iAOn8sDGcBfjuxv=W8y=QrZukjXUvo7@mail.gmail.com"
type="cite">On Wed, Feb 9, 2011 at 11:16, Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">On 8/02/2011 9:27 PM, bipin singh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi all,<br>
I am getting following during while running<br>
pdb2gmx for a RNA molecule....i am using amber99sb force
field parameters<br>
<br>
The details of the error is as:<br>
<br>
Fatal error:<br>
In the chosen force field there is no residue type for
'ARG' as a starting terminus<br>
For more information and tips for troubleshooting, please
check the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
</blockquote>
<br>
</div>
Sounds like you have an arginine residue. Why?<br>
<br>
Mark<br>
<font color="#888888">
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</div>
<br>
<br clear="all">
<br>
-- <br>
<font color="#3333ff"><i><font face="arial, helvetica, sans-serif">
<div>---------------------------------<br>
Thanks and regards<br>
</div>
<div><span style="font-family: arial; font-style: normal;"><i><font
face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div>
</font></i></font>
<div><font color="#3333ff" face="arial, helvetica, sans-serif"><i><br>
</i></font></div>
<br>
</blockquote>
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