Dear Mark,<br><br>I edited my pdb like this:<br>...<br>ATOM 41 N BOC 3 -1.862 5.210 5.333
<br>ATOM 42 H BOC 3 -2.325 4.344 5.618
<br>ATOM 43 CA BOC 3 -1.001 5.232 4.169
<br>ATOM 44 HA1 BOC 3 -0.540 6.235 4.026<br>ATOM 45 HA2 BOC 3 -0.172 4.511 4.360
<br>ATOM 46 CB BOC 3 -1.797 4.794 2.924
<br>ATOM 47 HB1 BOC 3 -2.244 3.809 3.204
<br>ATOM 48 CG1 BOC 3 -2.976 5.730 2.589<br>ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
<br>ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
<br>ATOM 51 CD2 BOC 3 0.120 5.408 1.353
<br>ATOM 52 HD2 BOC 3 0.357 6.277 1.986
<br>ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
<br>ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
<br>ATOM 55 CE2 BOC 3 0.881 5.182 0.197
<br>ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
<br>ATOM 57 CZ BOC 3 0.591 4.093 -0.639<br>ATOM 58 CG2 BOC 3 -0.935 4.544 1.698<br>ATOM 59 HG1 BOC 3 -3.530 5.331 1.707
<br>ATOM 60 HG2 BOC 3 -3.708 5.729 3.431
<br>ATOM 61 C BOC 3 -2.565 7.148 2.291
<br>ATOM 62 O BOC 3 -2.716 8.035 3.131
<br>ATOM 63 Cl BOC 3 1.525 3.816 -2.062
<br>END<br><br>and my .rtp file for [ BOC ] is:<br><br><span style="background-color: rgb(102, 204, 204);">[ BOC ]</span><br> <span style="background-color: rgb(255, 255, 153);">[ atoms ]</span><br> N opls_238 -0.500 1 <br>
H opls_241 0.300 1<br> CA opls_224B -0.005 1<br> HA1 opls_140 0.060 1<br> HA2 opls_140 0.060 1<br> CB opls_149 0.140 2<br> HB1 opls_140 0.060 2<br>
CG1 opls_145 -0.115 2<br> CD1 opls_145 -0.115 3<br> HD1 opls_146 0.115 3<br> CD2 opls_145 -0.115 4<br> HD2 opls_146 0.115 4<br> CE1 opls_145 -0.115 5<br>
HE1 opls_146 0.115 5<br> CE2 opls_145 -0.115 6<br> HE2 opls_146 0.115 6 <br> CZ opls_145 0.885 7<br> Cl opls_264 -1.000 7<br> CG2 opls_071 -0.005 8<br>
HG1 opls_140 0.060 8<br> HG2 opls_140 0.060 8<br> C opls_235 0.700 9<br> O opls_236 -0.700 9<br> <span style="background-color: rgb(255, 255, 153);">[ bonds ]</span><br>
N H<br> N CA<br> CA HA1<br> CA HA2<br> CA CB<br> CB HB1<br> CB CG1<br> CB CG2<br> CG1 CD1<br> CG1 CD2<br> CD1 HD1<br> CD1 CE1<br> CD2 HD2<br> CD2 CE2<br>
CE1 HE1<br> CE1 CZ<br> CE2 HE2<br> CE2 CZ<br> CZ Cl<br> CG2 HG1<br> CG2 HG2<br> CG2 C<br> C O<br> -C N<br><br>and still i got that error!<br><br><span style="background-color: rgb(102, 255, 153);">Fatal error:</span><br style="background-color: rgb(102, 255, 153);">
<span style="background-color: rgb(102, 255, 153);">Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1</span><br><br><div class="gmail_quote">On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 9/11/2010 8:19 PM, hengame fallah wrote:
<blockquote type="cite">Thanks Justin,<br>
actually the protein that i want to simulate consists of two amino
acids: PHE and BOC<br>
BOC is an unusual amino acid as you know.<br>
It has a Cl instead of HZ in PHE and has one extra CH2 in
comparison to PHE<br>
</blockquote>
<br></div>
So that probably means you'll have to pay care to the [bonds]
section in the .rtp file. The only bonds GROMACS knows about are the
ones in the .rtp. They have to be right. The errors below look like
you haven't done it right.<div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
I finally defined a residue BOC in opls .rtp file:<br>
<br>
[ BOC ]<br>
[ atoms ]<br>
N opls_238 -0.500 1 <br>
H opls_241 0.300 1<br>
CA opls_224B -0.005 1<br>
HA1 opls_140 0.060 1<br>
HA2 opls_140 0.060 1<br>
CB opls_149 0.140 2<br>
HB1 opls_140 0.060 2<br>
CG1 opls_145 -0.115 2<br>
CD1 opls_145 -0.115 3<br>
HD1 opls_146 0.115 3<br>
CD2 opls_145 -0.115 4<br>
HD2 opls_146 0.115 4<br>
CE1 opls_145 -0.115 5<br>
HE1 opls_146 0.115 5<br>
CE2 opls_145 -0.115 6<br>
HE2 opls_146 0.115 6 <br>
CZ opls_145 0.885 7<br>
Cl opls_264 -1.000 7<br>
CG2 opls_071 -0.005 8<br>
HG1 opls_140 0.060 8<br>
HG2 opls_140 0.060 8<br>
C opls_235 0.700 9<br>
O opls_236 -0.700 9<br>
<br>
the ending part of my PDB is:<br>
...<br>
ATOM 38 HE2 PHE 2 -6.946 8.455 4.409
<br>
ATOM 39 CZ PHE 2 -5.456 10.015 4.624
<br>
ATOM 40 HZ PHE 2 -5.887 10.646 3.828
<br>
ATOM 41 N BOC 3 -1.862 5.210 5.333
<br>
ATOM 42 H BOC 3 -2.325 4.344 5.618
<br>
ATOM 43 CA BOC 3 -1.001 5.232 4.169
<br>
ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
<br>
</blockquote>
<br></div></div>
HA2 is missing here, per your .rtp<div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">ATOM 45 CB BOC 3 -1.797 4.794 2.924
<br>
<span style="background-color: rgb(255, 102, 102);">ATOM 46
HB1 BOC 3 -2.244 3.809 3.204
</span><br>
ATOM 47 CG1 BOC 3 -2.976 5.730 2.589
<br>
ATOM 48 CG2 BOC 3 -0.935 4.544 1.698
<br>
ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
<br>
ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
<br>
ATOM 51 CD2 BOC 3 0.120 5.408 1.353
<br>
ATOM 52 HD2 BOC 3 0.357 6.277 1.986
<br>
ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
<br>
ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
<br>
ATOM 55 CE2 BOC 3 0.881 5.182 0.197
<br>
ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
<br>
ATOM 57 CZ BOC 3 0.591 4.093 -0.639
<br>
ATOM 58 C BOC 3 -2.565 7.148 2.291
<br>
ATOM 59 O BOC 3 -2.716 8.035 3.131
<br>
ATOM 60 CL BOC 3 1.525 3.816 -2.062
<br>
ATOM 61 HA2 BOC 3 -0.172 4.511 4.360
<br>
ATOM 62 HG1 BOC 3 -3.530 5.331 1.707
<br>
ATOM 63 HG2 BOC 3 -3.708 5.729 3.431<br>
<br>
Now i got t this error:<br>
...<br>
There are 1 chains and 0 blocks of water and 3 residues with 63
atoms<br>
<br>
chain #res #atoms<br>
1 ' ' 3 63 <br>
<br>
All occupancy fields zero. This is probably not an X-Ray structure<br>
Opening library file /usr/share/gromacs/top/ffoplsaa.atp<br>
Atomtype 1<br>
Reading residue database... (ffoplsaa)<br>
Opening library file /usr/share/gromacs/top/ffoplsaa.rtp<br>
Residue 57<br>
Sorting it all out...<br>
Opening library file /usr/share/gromacs/top/ffoplsaa.hdb<br>
Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb<br>
Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb<br>
<br>
Back Off! I just backed up topol.top to ./#topol.top.69#<br>
Processing chain 1 (63 atoms, 3 residues)<br>
There are 3 donors and 3 acceptors<br>
There are 4 hydrogen bonds<br>
Checking for duplicate atoms....<br>
Opening library file /usr/share/gromacs/top/specbond.dat<br>
7 out of 7 lines of specbond.dat converted succesfully<br>
N-terminus: NH3+<br>
C-terminus: COO-<br>
Now there are 3 residues with 68 atoms<br>
Making bonds...<br>
Warning: Long Bond (52-53 = 0.334847 nm)<br>
Warning: Long Bond (52-55 = 0.334912 nm)<br>
Warning: Long Bond (63-64 = 0.271173 nm)<br>
Warning: Long Bond (63-65 = 0.347808 nm)<br>
Warning: Long Bond (63-66 = 0.31288 nm)<br>
</blockquote>
<br></div></div>
This is telling you the connectivity in your .rtp doesn't match the
spatial arrangement very well. Go back and check the .rtp file.<div class="im"><br>
<br>
<blockquote type="cite">Opening library file
/usr/share/gromacs/top/aminoacids.dat<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.7<br>
Source code file: ../../../../src/kernel/add_par.c, line: 233<br>
<br>
<span style="background-color: rgb(255, 255, 0);">Fatal error:</span><br>
Atom <span style="background-color: rgb(255, 102, 102);">HB11</span>
not found in rtp database in residue BOC, it looks a bit like HB1<br>
</blockquote>
<br></div>
pdb2gmx is probably hopelessly confused by now. Fix the other issues
and try again.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
-------------------------------------------------------<br>
...<br>
<br>
What should i do?<br>
<br>
<br></blockquote></div></div></div></blockquote></div>