Hi Justin,<div><br></div><div>Thanks for your reply, i have no particular choice i was using it for my other work and just started with it.</div><div><br></div><div>Now i tried it again with spc model,</div><div><br></div>
<div>I still get the following error.</div><div>++++++++++++++++++++++++++++++++++++++++++++++</div><div><div>Program grompp, VERSION 4.5.4</div><div>Source code file: toppush.c, line: 1166</div><div><br></div><div>Fatal error:</div>
<div>Atomtype OWT3 not found</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div>
<div>++++++++++++++++++++++++++++++++++++++++++++++</div><div><br></div><div>I could see these atoms are defined in .itp file of gromos force filed, but i suspect some thing is going wrong with atom types in .atp file.</div>
<div><br></div><div>any suggestions? </div><div><br></div><div>Thanks</div><div>Srinivs. </div><br><div class="gmail_quote">On Fri, Jul 22, 2011 at 5:11 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
jampani srinivas wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs users,<br>
<br>
I am trying to run a fullerene simulaton in TIP4P water model, i am using the "c70_G53a6.itp <<a href="http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp" target="_blank">http://tfy.tkk.fi/soft/<u></u>downloads/files/c70_G53a6.itp</a>><u></u>" file downloaded from <a href="http://tfy.tkk.fi/soft/downloads/" target="_blank">http://tfy.tkk.fi/soft/<u></u>downloads/</a>. i have added TIP4P water model using genbox command, later when i am trying to generate .tpr file for energy minimization it gives me the following error. <br>
------------------------------<u></u>-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: toppush.c, line: 1166<br>
<br>
Fatal error:<br>
Atomtype OWT4 not found<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/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
<br>
I looked up in the mailing list and found many helpful comments but i could not resolve the problem, i searched in the tip4p.itp file of gromos force field and i could see that tip4p water model is defined in that file, but i could not find the atom types defined in atomtypes.atp file. when i try to enter the atom types for some reason it does not read my entries. <br>
</blockquote>
<br>
This may or may not be related to a bug that has been fixed in the development version of the code. Simply adding OWT4 into atomtypes.atp is insufficient; you need to add nonbonded parameters in ffnonbonded.itp as well. Without seeing the actual error message(s) you're getting, I don't dare guess further.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
here is my .top file<br>
<br>
; The force field files to be included<br>
<br>
#include "ffG53a6.itp"<br>
<br>
[ moleculetype ]<br>
#include "fullerene.itp"<br>
<br>
; Include water topology<br>
#include "tip4p.itp"<br>
<br>
[ system ]<br>
Fullerene in Water<br>
<br>
[ molecule ]<br>
FUL 1<br>
SOL 1696<br>
<br>
Can anybody help me?<br>
<br>
</blockquote>
<br>
Is there a particular reason you need to use TIP4P? The Gromos force fields were parameterized with SPC water, so that's what is expected to work. In principle, you should be able to use any water model you want, but you still have to demonstrate that it's a valid approach.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br><font color="#000099"><font face="'comic sans ms', sans-serif">*********************************************<br><b>J. Srinivasa Rao <br>Post-doctoral Research Associate<br>
Computational Biophysics Group<br>Department of Physics, Drexel University<br>3141 Chestnut St, Philadelphia, PA 19104<br>Ph: 215-895-1989<br>Web:<a href="http://jsrao.web.officelive.com/default.aspx" target="_blank">http://jsrao.web.officelive.com/default.aspx</a></b><br>
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