Dear Justin,<br><br>I manually specify termini. I choosed "None" but I have the same error.<br><br>Fatal error:<br>atom C not found in residue 13NH2 while combining tdb and rtp<br><br><br><div class="gmail_quote">
22 Ocak 2011 00:45 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;">
Dear justin,<br>
<br>
I looked at the pdb file. No NH2 reside contains carbon atom.<br>
<br>
What should I do?<br>
</blockquote>
<br></div>
In this case, you need to manually specify termini. Choose "None" to allow your capping groups to be built properly.<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;">
<br>
22 Ocak 2011 00:18 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><div>
</div><div class="h5"><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
I think I need to edit the aminoacids.rtp file in gromos43a1.ff<br>
folder as far as I understand from mailing list. I am using 43a1<br>
forcefield. I do not understand what kind of changes should I do.<br>
<br>
<br>
You do not need to modify the .rtp file, you need to modify your<br>
coordinate file, as I said before. The fatal error indicates that<br>
you have included a C atom in an NH2 residue, which is just a<br>
neutral amine and contains no carbon, as should be clear from the<br>
.rtp file.<br>
<br>
-Justin<br>
<br>
*the aminoacids.rtp file:*<br>
<br>
[ ACE ]<br>
[ atoms ]<br>
CA CH3 0.000 0<br>
C C 0.380 1<br>
O O -0.380 1<br>
[ bonds ]<br>
C CA gb_26<br>
C O gb_4<br>
C +N gb_9<br>
[ angles ]<br>
CA C O ga_30<br>
CA C +N ga_18<br>
O C +N ga_32<br>
[ impropers ]<br>
C CA +N O gi_1<br>
<br>
[ NH2 ]<br>
[ atoms ]<br>
N NT -0.83 0<br>
H1 H 0.415 0<br>
H2 H 0.415 0<br>
[ bonds ]<br>
N H1 gb_2<br>
N H2 gb_2 -C N gb_8<br>
[ angles ]<br>
-O -C N ga_32<br>
-CA -C N ga_18<br>
-C N H1 ga_22<br>
-C N H2 ga_22<br>
H1 N H2 ga_23<br>
[ dihedrals ]<br>
-CA -C N H1 gd_4<br>
[ impropers ]<br>
-C -O N -CA gi_1<br>
N H1 H2 -C gi_1<br>
<br>
[ ALA ]<br>
[ atoms ]<br>
N N -0.28000 0<br>
H H 0.28000 0<br>
CA CH1 0.00000 1<br>
CB CH3 0.00000 1<br>
C C 0.380 2<br>
O O -0.380 2<br>
[ bonds ]<br>
N H gb_2 N CA gb_20 CA C gb_26<br>
C O gb_4 C +N gb_9 CA CB gb_26 2011/1/21 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div></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><div></div><div class="h5"><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>
Gromacs 4.5.3<br>
pdb2gmx -f xxx.pdb -water spc<br>
select Force Field:9<br>
*Fatal error:*<br>
atom C not found in buiding block 13NH2 while combining<br>
tdb and rtp<br>
For more information and tips for troubleshooting, please<br>
check<br>
the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
How can I fixed this error?<br>
<br>
<br>
You have a carbon atom in a residue that should only contain NH2.<br>
Refer to the .rtp file for what is expected, then make a<br>
suitable<br>
structure that conforms to those requirements.<br>
<br>
This has been asked and answered hundreds of times, so please<br>
make<br>
use of the mailing list search. You would have gotten your<br>
answer<br>
in minutes rather than hours.<br>
<br>
-Justin<br>
<br>
<br>
Thanks in advance<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></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">
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<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>
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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>
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