Sara,<br>
<br>
You might want to correspond with the Pande group on this, as they're the ones who put out the port. <br>
<br>
I had a similar problem with Cl- ions and, as a temporary solution,
modified the ions.itp file in the top directory to have an #ifdef
_FF_AMBER section specifying the appropriate ion definitions (copied
from earlier in the ions.itp file but changing the atom types to the
amber atom types -- i.e. CL- is amber94_30). My conclusion was that no
ion parameters were being loaded when _FF_AMBER was defined, so I
thought this was necessary. I remember corresponding with Eric Sorin
(Pande group) on this and he had some alternative method of setting up
systems where this wasn't a problem, I think. <br>
<br>
Anyway, you'll probably need to talk to them, as the Amber FF is not a
part of Gromacs, so in general you probably won't get support from this
list.<br>
<br>
David<br>
<br><br><div><span class="gmail_quote">On 10/26/05, <b class="gmail_sendername">sara pistolesi</b> <<a href="mailto:sarapistolesi@hotmail.com">sarapistolesi@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div style=""><p>Dear alll,</p>
<p>I'm trying to carry out a MD simulation on a small RNA
molecule. Then I've downloaded the ffamber99 force field port for
gromacs ,modified my pdb file and runed pdb2gmx. I've solvated the
system using ffamber_tip4p files and neutralized the system charge
using Na+ ions.</p>
<p>But when I run grompp command for energy minimization the software
is not able to recognize Na+ ions (I tryed to write it in all possible
ways, NA+, NA, Na+ and Na, but the results are the same).</p>
<p>How may I do?</p>
<p>Thanks in advance.</p>
<p>Bests,<br><font face="Lucida Handwriting, Cursive">Sara Pistolesi</font></p></div>
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