I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as far as I understand from mailing list. I am using 43a1 forcefield. <span id="result_box" class="" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps"></span></span><span id="result_box" class="" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">I</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">do not understand</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">what</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">kind of</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">changes</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">should</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">I do.</span></span><br>
<br><b>the aminoacids.rtp file:</b><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 <br> -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 <br> N CA gb_20 <br> CA C gb_26 <br>
C O gb_4 <br> C +N gb_9 <br> CA CB gb_26 <br><br><div class="gmail_quote">2011/1/21 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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 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 tdb and rtp<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/Documentation/Errors</a><br>
<br>
<br>
How can I fixed this error?<br>
<br>
</blockquote>
<br></div>
You have a carbon atom in a residue that should only contain NH2. Refer to the .rtp file for what is expected, then make a suitable structure that conforms to those requirements.<br>
<br>
This has been asked and answered hundreds of times, so please make use of the mailing list search. You would have gotten your answer in minutes rather than hours.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br></div>
-- <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>Ahmet YILDIRIM<br>