Thanks Justin. Problem is solved.<br><br>.itp file:<br>[ moleculetype ]<br>; Name nrexcl<br>TRS 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 TRS O1 1 -0.119 15.9994 <br>
2 H 1 TRS H13 1 0.032 1.0080 <br> 3 CH2 1 TRS C1 1 0.087 14.0270 <br> 4 <b>CCL4 </b> 1 TRS C 2 0.055 12.0110 <br> 5 CH2 1 TRS C3 2 0.049 14.0270 <br>
..<br><br>.newitp<br>[ moleculetype ]<br>; Name nrexcl<br>TRS 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 TRS O1 1 -0.119 15.9994 <br> 2 H 1 TRS H13 1 0.032 1.0080 <br>
3 CH2 1 TRS C1 1 0.087 14.0270 <br> 4 <b>CCl4 </b> 1 TRS C 2 0.055 12.0110 <br> 5 CH2 1 TRS C3 2 0.049 14.0270 <br>...<br><div class="gmail_quote">
29 Mart 2011 16:41 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br><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"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Then, what should I do?<br>
<br>
</blockquote>
<br></div>
You've somehow created a topology that does not conform to the requirements of the force field. Fix it so that it does.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
29 Mart 2011 16:36 tarihinde Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> yazdı:<div class="im">
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear Justin,<br>
<br>
<br>
There is "CCl4 12.011 ; carbon in carbontetrachloride<br>
(solvent)" in the gromos43a1.ff/atomtypes.atp file.<br>
But I still have the error "Atomtype CCL4 not found".<br>
<br>
<br>
Exactly as I said, capitalization is your issue. CCl4 and CCL4 are<br>
not the same.<br>
<br>
-Justin<br>
<br>
2011/3/29 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><div class="im"><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>><br>
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear users,<br>
<br>
Force field: 43a1<br>
water model: spc<br>
<br>
After this command:grompp -f em.mdp -p topol.top -c<br>
solvated.gro<br>
-o em.tpr<br>
<br>
I have the following error:<br>
<br>
Fatal error:<br>
Atomtype CCL4 not found<br>
<br>
What should I do?<br>
<br>
<br>
Use an appropriate atom type. The issue is probably<br>
capitalization<br>
somewhere, i.e. CCl4 rather than CCL4. See atomtypes.atp.<br>
<br>
-Justin<br>
<br>
<br>
-- Ahmet YILDIRIM<br>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
231-9080<br>
<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>
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-- Ahmet YILDIRIM<br>
<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> <<a href="http://vt.edu" target="_blank">http://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>
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</div></div></blockquote><div><div></div><div class="h5">
<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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