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>
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>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>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>
-------------------------------------------------------<br>...<br><br>What should i do?<br><br><br><div class="gmail_quote">On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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><div></div><div class="h5"><br>
<br>
hengame fallah wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
I'm using the OPLS force field.<br>
<br>
[ PHE ]<br>
[ atoms ]<br>
N opls_238 -0.500 1<br>
H opls_241 0.300 1<br>
CA opls_224B 0.140 1<br>
HA opls_140 0.060 1<br>
CB opls_149 -0.005 2<br>
HB1 opls_140 0.060 2<br>
HB2 opls_140 0.060 2<br>
CG 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 -0.115 7<br>
HZ opls_146 0.115 7<br>
C opls_235 0.500 8<br>
O opls_236 -0.500 8<br>
<br>
I want to attach "CL" atom instead of HZ<br>
i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and top files.<br>
What should i do to get rid of this HZ and attach CL instead.<br>
</blockquote>
<br></div></div>
If the .rtp entry says to build PHE with those constituent atoms, it will do so. You can make a custom .rtp entry that has CL instead of HZ.<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;">
(I edited top and gro files and remove HZ from them, it seemed to work properly at first, but when i tried to do energy minimization, it had errors in top file<br>
and i realized that it couldn't recognized the bond between CL and CZ):<br>
<br>
ERROR 1 [file topol.top, line 150]:<br>
No default Bond types<br>
<br>
<br>
ERROR 2 [file topol.top, line 422]:<br>
No default Angle types<br>
<br>
<br>
ERROR 3 [file topol.top, line 423]:<br>
No default Angle types<br>
<br>
</blockquote>
<br></div>
All of these errors indicate that OPLS cannot accommodate such a species. Making ad hoc changes to the topology often does this. Look at what these lines contain and you will be able to identify the relevant parameters that are missing.<br>
<br>
<snip><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;">
66 opls_401 5 CL CL 26 -1 35.453 ; qtot -1.06<br>
</blockquote>
<br></div>
I would seriously question the validity of doing this. Is it really correct to put (essentially) a Cl- ion on a Phe ring and call it correct? Proper parameterization is a very challenging task, and I doubt what you've proposed here is valid.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><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;">
...<br>
[ bonds ]<br>
...<br>
59 66 1<br>
60 61 1<br>
60 62 1<br>
63 64 1<br>
63 65 1<br>
...<br>
[ angles ]<br>
...<br>
58 57 59 1<br>
55 59 57 1<br>
55 59 66 1<br>
57 59 66 1<br>
45 60 61 1<br>
45 60 62 1<br>
61 60 62 1<br>
64 63 65 1<br>
...<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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