Hi!<br>I am using the gromos9643a1 forcefield and the chloride is described as given below in the rtp file. I have described the CL as CL- in my pdb input file and still it is not accepting! I am using V 4.0.5<br><br>[ CL- ]<br>
[ atoms ]<br> CL CL- -1.00000 0<br> [ bonds ]<br> [ angles ] <br>; ai aj ak gromos type<br> [ impropers ] <br>; ai aj ak al gromos type<br> [ dihedrals ] <br>; ai aj ak al gromos type<br>
<br><br><div class="gmail_quote">On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><br>
<br>
jayant james wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi!<br>
The protein I am attempting to simulate has a CL atom. When I run pdb2gmx I get the following error message. Any help in overcoming this problem would be appreciated.<br>
Thanks<br>
James ------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0<br>
Source code file: pdb2gmx.c, line: 429<br>
<br>
Fatal error:<br>
Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms<br>
while sorting atoms<br>
-------------------------------------------------------<br>
</blockquote>
<br></div>
You haven't told us which force field you're trying to use, but I'm guessing that the chloride .rtp entry is probably named "CL" instead of "CL-" (which is used by the ffG* force fields). You can check the .rtp file to be sure.<br>
<br>
Also, I would strongly suggest upgrading to version 4.0.7 - there have been numerous bug fixes and performance upgrades since version 4.0.<br>
<br>
-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;">
<br>
<br>
-- <br>
Jayasundar Jayant James<br>
<br>
<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">www.chick.com/reading/tracts/0096/0096_01.asp</a> <<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">http://www.chick.com/reading/tracts/0096/0096_01.asp</a>>)<br>
<br>
</blockquote>
<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>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br>