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On 16/11/2010 9:04 PM, hengame fallah wrote:
<blockquote
cite="mid:AANLkTinOXU2uyGPv7Cqj_PWVf2T0s180O0AaccMJPu+r@mail.gmail.com"
type="cite">Thank you very much, Mark!<br>
Now i have errors from my .top file after grompp command.<br>
The question is that why in pdb2gmx, editconf ,genbox and make_ndx
steps i don't see these errors:<br>
<br>
<span style="background-color: rgb(255, 204, 153);">...</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">processing
topology...</span><br style="background-color: rgb(255, 204,
153);">
<span style="background-color: rgb(255, 204, 153);">Opening
library file /usr/share/gromacs/top/ffoplsaa.itp</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening
library file /usr/share/gromacs/top/ffoplsaanb.itp</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening
library file /usr/share/gromacs/top/ffoplsaabon.itp</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Generated
332520 of the 332520 non-bonded parameter combinations</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Generating 1-4
interactions: fudge = 0.5</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Generated
332520 of the 332520 1-4 parameter combinations</span><br
style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 1 [file
topol.top, line 412]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Angle types</span><br style="background-color: rgb(255, 204,
153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 2 [file
topol.top, line 567]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 3 [file
topol.top, line 570]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 4 [file
topol.top, line 573]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 5 [file
topol.top, line 580]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 6 [file
topol.top, line 581]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">ERROR 7 [file
topol.top, line 582]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> No default
Ryckaert-Bell. types</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening
library file /usr/share/gromacs/top/spc.itp</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Opening
library file /usr/share/gromacs/top/ions.itp</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Excluding 3
bonded neighbours molecule type 'Protein'</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Excluding 2
bonded neighbours molecule type 'SOL'</span><br
style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">NOTE 1 [file
topol.top, line 664]:</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> System has
non-zero total charge: 6.000000e-02</span><br
style="background-color: rgb(255, 204, 153);">
</blockquote>
<br>
0.06 means your residue's charges do not add to zero, and they
should.<br>
<br>
<blockquote
cite="mid:AANLkTinOXU2uyGPv7Cqj_PWVf2T0s180O0AaccMJPu+r@mail.gmail.com"
type="cite"><span style="background-color: rgb(255, 204, 153);">
</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">processing
coordinates...</span><br style="background-color: rgb(255, 204,
153);">
<span style="background-color: rgb(255, 204, 153);">double-checking
input for internal consistency...</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">renumbering
atomtypes...</span><br style="background-color: rgb(255, 204,
153);">
<span style="background-color: rgb(255, 204, 153);">converting
bonded parameters...</span><br style="background-color: rgb(255,
204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">There was 1
note</span><br style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">-------------------------------------------------------</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Program
grompp, VERSION 4.0.7</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Source code
file: ../../../../src/kernel/grompp.c, line: 986</span><br
style="background-color: rgb(255, 204, 153);">
<br style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">Fatal error:</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);">There were 7
errors in input file(s)</span><br>
<br>
<b>topol.top:</b><br>
...<br>
<span style="background-color: rgb(255, 204, 153);">43</span>
opls_238 3 BOC <span style="background-color:
rgb(255, 204, 153);">N</span> 17 -0.5 14.0067 ;
qtot 0.5<br>
44 opls_241 3 BOC H 17 0.3
1.008 ; qtot 0.8<br>
<span style="background-color: rgb(255, 204, 153);">45</span>
opls_283 3 BOC <span style="background-color:
rgb(255, 204, 153);">CA</span> 17 0.04 12.011 ;
qtot 0.84<br>
<span style="background-color: rgb(255, 204, 153);">46</span>
opls_140 3 BOC <span style="background-color: rgb(255,
204, 153);">HA1</span> 17 0.06 1.008 ; qtot 0.9<br>
<span style="background-color: rgb(255, 204, 153);">47</span>
opls_140 3 BOC <span style="background-color: rgb(255,
204, 153);"> HA2</span> 17 0.06 1.008 ; qtot
0.96<br>
<span style="background-color: rgb(255, 204, 153);">48</span>
opls_149 3 BOC <span style="background-color:
rgb(255, 204, 153);">CB</span> 18 0.055 12.011 ;
qtot 1.015<br>
49 opls_140 3 BOC HB 18 0.06
1.008 ; qtot 1.075<br>
50 opls_145 3 BOC CG1 18 -0.115
12.011 ; qtot 0.96<br>
51 opls_145 3 BOC CD1 19 -0.115
12.011 ; qtot 0.845<br>
52 opls_146 3 BOC HD1 19 0.115
1.008 ; qtot 0.96<br>
53 opls_145 3 BOC CD2 20 -0.115
12.011 ; qtot 0.845<br>
54 opls_146 3 BOC HD2 20 0.115
1.008 ; qtot 0.96<br>
55 opls_145 3 BOC CE1 21 -0.115
12.011 ; qtot 0.845<br>
56 opls_146 3 BOC HE1 21 0.115
1.008 ; qtot 0.96<br>
57 opls_145 3 BOC CE2 22 -0.115
12.011 ; qtot 0.845<br>
58 opls_146 3 BOC HE2 22 0.115
1.008 ; qtot 0.96<br>
59 opls_145 3 BOC CZ 23 1
12.011 ; qtot 1.96<br>
60 opls_264 3 BOC Cl 23 -1
35.453 ; qtot 0.96<br>
<span style="background-color: rgb(255, 204, 153);">61</span>
opls_224B 3 BOC <span style="background-color: rgb(255,
204, 153);">CG2</span> 24 -0.12 12.011 ; qtot
0.84<br>
<span style="background-color: rgb(255, 204, 153);">62</span>
opls_140 3 BOC <span style="background-color: rgb(255,
204, 153);">HG1</span> 24 0.06 1.008 ; qtot 0.9<br>
<span style="background-color: rgb(255, 204, 153);">63</span>
opls_140 3 BOC <span style="background-color: rgb(255,
204, 153);">HG2</span> 24 0.06 1.008 ; qtot
0.96<br>
<span style="background-color: rgb(255, 204, 153);">64</span>
opls_271 3 BOC <span style="background-color: rgb(255,
204, 153);"> C</span> 25 0.7 12.011 ; qtot
1.66<br>
65 opls_272 3 BOC O1 25 -0.8
15.9994 ; qtot 0.86<br>
66 opls_272 3 BOC O2 25 -0.8
15.9994 ; qtot 0.06<br>
...<br>
[ angles ]<br>
...<br>
<span style="background-color: rgb(255, 204, 204);">line 412</span>:
45 48 61 1<br>
...<br>
[ dihedrals ]<br>
...<br>
<span style="background-color: rgb(255, 204, 204);">line 567</span>:
43 45 48 61 3 <br>
...<br>
<span style="background-color: rgb(255, 204, 204);">line 570</span>:
46 45 48 61 3 <br>
...<br>
<span style="background-color: rgb(255, 204, 204);">line 573</span>:
47 45 48 61 3 <br>
...<br>
<span style="background-color: rgb(255, 204, 204);">line 580</span>:
45 48 61 62 3 <br>
<span style="background-color: rgb(255, 204, 204);">line 581</span>:
45 48 61 63 3 <br>
<span style="background-color: rgb(255, 204, 204);">line 582</span>:
45 48 61 64 3 <br>
...<br>
<br>
it seems that "45 48 61" is the problem. CA CB CG2 <br>
Where i should define angle type for it?<br>
</blockquote>
<br>
Those three atoms have types. The type of function to put on an
angle whose three atoms have given types is defined in the force
field. Evidently, there isn't one for the types of these atoms. This
relates to choosing your atom types properly, like I've said twice
before now. Go and look up their types in the .rtp, and then look up
in the .atp what environments the types for which they were
parameterized, and see what your non sequitur is.<br>
<br>
Mark<br>
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