Thanks for your help.....<br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 11:44, 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="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 9/02/2011 4:56 PM, bipin singh wrote:
<blockquote type="cite">Sir,<br>
Actually ARG is present as a ligand bound to RNA molecule....<br>
</blockquote>
<br></div>
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><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">On Wed, Feb 9, 2011 at 11:16, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>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 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>
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>
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<br>
</blockquote>
<br>
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---------------------------------<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>
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