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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I suspect you still use #include “ffoplsaa.itp”
in your topology, i.e. input.top.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Anyway, you may use –pp for grompp
to check processed topology and find whether atom type CT is included.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yang Ye<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Luciano Costa<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, February 15, 2006
1:12 AM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Fatal error:
Atomtype 'CT' not found!</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br clear=all>
Hi gmx' users,<br>
<br>
I have tried running gromacs with a diferent force field. Adjusted by us.<br>
<br>
Firstly, I have setted in FF.dat, the new force field, as following:<br>
7<br>
ffG43a1 GROMOS96 43a1 Forcefield (official distribution)<br>
ffG43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)<br>
ffG43a2 GROMOS96 43a2 Forcefield (development) (improved alkane
dihedrals)<br>
ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
ffoplsaa_new OPLSAA (modificado por
luciano) <---------- LOOK THIS !<br>
ffgmx Gromacs Forcefield (see manual)<br>
ffgmx2 gmx Forcefield with hydrogens for NMR stuff (Do NOT use for
new runs)<br>
<br>
<br>
Then I generated the new files ffoplsaa_new* (</span></font><strong><b><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>.rtp, .atp,
-n.tdb, bon.itp etc.) (9 total).</span></font></b></strong><b><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial;font-weight:bold'><br>
<br>
<strong><b><font face=Arial><span style='font-family:Arial'>When I tried run
grommp with:</span></font></b></strong><br>
<br>
<strong><b><font face=Arial><span style='font-family:Arial'>prompt> grompp
-v -f grompp.mdp -c input.gro -p input.top -o -debug</span></font></b></strong><br>
<br>
<strong><b><font face=Arial><span style='font-family:Arial'>It is shown this
message:</span></font></b></strong><br>
<br>
<strong><b><font face=Arial><span style='font-family:Arial'>#########################################################</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Back Off! I just
backed up mdout.mdp to ./#mdout.mdp.8#</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>checking input for
internal consistency...</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>calling /lib/cpp...</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>processing
topology...</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Generated 120 of
the 120 non-bonded parameter combinations</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Generating 1-4
interactions: fudge = 0.5</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Generated 120 of
the 120 1-4 parameter combinations</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Cleaning up
temporary file gromppTtNKGJ</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>Fatal error:
Atomtype 'CT' not found!</span></font></b></strong><br>
<strong><b><font face=Arial><span style='font-family:Arial'>########################################################</span></font></b></strong><br>
</span></font></b><br>
The atomtype CT is defined in *.atp, *.rtp, ffoplsaa_newbon.itp and
ffoplsaa_newnb.itp.<br>
I also checked ffoplsaa_new.itp and it is as shown below:<br>
prompt> cat ffoplsaa_new.itp<br>
#define _FF_OPLS<br>
#define _FF_OPLSAA<br>
<br>
; This force field uses a format that requires Gromacs 3.1.4 or later.<br>
;<br>
; References for the OPLS-AA force field:<br>
;<br>
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,<br>
; J. Am. Chem. Soc. 118, 11225-11236 (1996).<br>
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).<br>
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).<br>
; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).<br>
; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).<br>
; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).<br>
; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys.
Chem. B 105, 6474 (2001).<br>
;<br>
<br>
[ defaults ]<br>
; nbfunc
comb-rule gen-pairs
fudgeLJ fudgeQQ<br>
1
3
yes 0.5
0.5<br>
<br>
;#include "ffoplsaanb.itp"<br>
;#include "ffoplsaabon.itp"<br>
#include "ffoplsaa_newnb.itp"<br>
#include "ffoplsaa_newbon.itp"<br>
<br>
What should I do in this case ?! Why the error message ?! <br>
<br>
Best regards,<br>
<br>
Luciano.<br>
<br>
-- <br>
### Luciano Tavares da Costa ###<br>
## <br>
## 100 % Linux<br>
############################# <o:p></o:p></p>
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