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On 14/11/2010 7:26 PM, hengame fallah wrote:
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">Dear Mark,<br>
I think that i couldn't explain my problem clearly, however i have
changed my .rtp but i don't know how should be my .hdb file.<br>
<br>
a) The structure of <b><u>BOC</u></b> is: <b>-<span
style="color: rgb(102, 0, 0);">C</span><span style="color:
rgb(102, 102, 0);">O</span>-<span style="color: rgb(102, 0,
0);">C</span><span style="color: rgb(102, 51, 102);">H2</span>-<span
style="color: rgb(102, 0, 0);">C</span><span style="color:
rgb(102, 51, 102);">H</span>(<span style="color: rgb(102, 0,
0);">C6</span><span style="color: rgb(102, 51, 102);">H5</span><span
style="color: rgb(51, 51, 0);">Cl</span>)-<span style="color:
rgb(102, 0, 0);">C</span><span style="color: rgb(102, 51,
102);">H2</span>-<span style="color: rgb(0, 0, 102);">N</span><span
style="color: rgb(102, 51, 102);">H</span>-</b><br>
</blockquote>
<br>
Great.<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">
b) This is the new charges:<br>
<span style="background-color: rgb(255, 204, 153);">[ BOC ]</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> [ atoms ]</span><br
style="background-color: rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> N
opls_238 -0.500 1 </span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> H
opls_241 0.300 1</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CA
opls_224B 0.080 1</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HA1
opls_140 0.060 1</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HA2
opls_140 0.060 1</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CB
opls_149 0.055 2</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HB
opls_140 0.060 2</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CG1
opls_145 -0.115 2</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CD1
opls_145 -0.115 3</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HD1
opls_146 0.115 3</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CD2
opls_145 -0.115 4</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HD2
opls_146 0.115 4</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CE1
opls_145 -0.115 5</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HE1
opls_146 0.115 5</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CE2
opls_145 -0.115 6</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HE2
opls_146 0.115 6 </span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CZ
opls_145 1.000 7</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> Cl
opls_264 -1.000 7</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> CG2
opls_071 -0.120 8</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HG1
opls_140 0.060 8</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> HG2
opls_140 0.060 8</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> C
opls_235 0.700 9</span><br style="background-color:
rgb(255, 204, 153);">
<span style="background-color: rgb(255, 204, 153);"> O
opls_236 -0.700 9</span><br>
</blockquote>
<br>
This looks much better.<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">c) charge for CG1 in PHE (in OPLS .rtp) is negative,
too.<br>
</blockquote>
<br>
OK<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">d) Would you explain for me that what is wrong in my
atom types?<br>
</blockquote>
<br>
No. My point last email was that you may need to consider what atom
types are suitable for your backbone methylene C. I don't know what
is suitable. You will have to look at the .atp file and perhaps read
OPLS/AA papers.<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">
e) As you see in the error, at first there are 63 residues (like
my pdb) but when when it adds COO- and NH3+ there are 69 residues!
it should add only one "O" (for COO-) and two "H"s for (NH3+) i
think.<br>
</blockquote>
<br>
Well, what do the .tdb files say? You should model these for BOC
upon the PHE ones, of course. You will need to have read the parts
of chapter 5 that pertain to the .hdb and .tdb files.<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite">
<br>
<span style="background-color: rgb(204, 255, 255);">There are 1
chains and 0 blocks of water and <span style="background-color:
rgb(255, 204, 204);">3</span> residues with <span
style="background-color: rgb(255, 204, 204);">63</span> atoms</span><br
style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);"> chain #res
#atoms</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);"> 1 ' '
3 63 </span><br style="background-color: rgb(204, 255,
255);">
<br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">All occupancy
fields zero. This is probably not an X-Ray structure</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/ffoplsaa.atp</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Atomtype 1</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Reading
residue database... (ffoplsaa)</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/ffoplsaa.rtp</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Residue 57</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Sorting it all
out...</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/ffoplsaa.hdb</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/ffoplsaa-n.tdb</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/ffoplsaa-c.tdb</span><br
style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Back Off! I
just backed up topol.top to ./#topol.top.3#</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Processing
chain 1 (63 atoms, 3 residues)</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">There are 3
donors and 3 acceptors</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">There are 4
hydrogen bonds</span><br style="background-color: rgb(204, 255,
255);">
<span style="background-color: rgb(204, 255, 255);">Checking for
duplicate atoms....</span><br style="background-color: rgb(204,
255, 255);">
<span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/specbond.dat</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">7 out of 7
lines of specbond.dat converted succesfully</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">N-terminus:
NH3+</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">C-terminus:
COO-</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(255, 204, 204);">Now there are
3 residues with 69 atoms</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Making
bonds...</span><br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long
Bond (53-54 = 0.334847 nm)</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long
Bond (53-56 = 0.334912 nm)</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long
Bond (64-65 = 0.271173 nm)</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long
Bond (64-66 = 0.347808 nm)</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Warning: Long
Bond (64-67 = 0.31288 nm)</span><br style="background-color:
rgb(204, 255, 255);">
</blockquote>
<br>
These warnings are still suggestive that your atom coordinates are
labelled inappropriately in your coordinate file.<br>
<br>
<blockquote
cite="mid:AANLkTim-ws7VdJ2sdcLtQom6gyyXB1c=7ZnYY81-wNsa@mail.gmail.com"
type="cite"><span style="background-color: rgb(204, 255, 255);">Opening
library file /usr/share/gromacs/top/aminoacids.dat</span><br
style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">-------------------------------------------------------</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Program
pdb2gmx, VERSION 4.0.7</span><br style="background-color:
rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Source code
file: ../../../../src/kernel/add_par.c, line: 233</span><br
style="background-color: rgb(204, 255, 255);">
<br style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Fatal error:</span><br
style="background-color: rgb(204, 255, 255);">
<span style="background-color: rgb(204, 255, 255);">Atom HB1 not
found in rtp database in residue BOC, it looks a bit like HB</span><br>
</blockquote>
<br>
I think your .hdb is still trying to add two hydrogens to CB.<br>
<br>
Mark<br>
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