Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have "residues" in my system, because I am not modeling a protein. So I am not sure what to put in the residue name column. Gromacs does work on molecules that are not proteins correct? My molecules are histidine like so I tried putting HIS as the residue name, but I got the error:<br>
<br>"Fatal error:<br>Residue 'H' not found in residue topology database"<br><br>When I dont put anything in that column I get the error:<br><br>"Fatal error:<br>Residue '' not found in residue topology database"<br>
<br>And when I just generically call everything solvent and put SOL in that column I get:<br><br>"Fatal error:<br>Residue 'S' not found in residue topology database"<br><br>You get the picture here. Does anyone have any solutions to my residue naming problem? Thank you.<br>
<br>here is my pdb file:<br><br>HETATM 1 CT 2 -4.438 3.334 2.988<br>HETATM 2 CT 2 0.588 3.313 0.517<br>HETATM 3 CT 2 5.476 3.310 -2.216<br>HETATM 4 HC 2 -4.134 2.590 3.731<br>
HETATM 5 HC 2 -5.525 3.438 3.047<br>HETATM 6 HC 2 -3.996 4.291 3.276<br>HETATM 7 HC 2 1.480 3.111 1.117<br>HETATM 8 HC 2 -0.266 3.349 1.200<br>
HETATM 9 HC 2 0.702 4.307 0.076<br>HETATM 10 HC 2 6.375 3.525 -1.633<br>HETATM 11 HC 2 4.648 3.862 -1.761<br>HETATM 12 HC 2 5.628 3.709 -3.223<br>
HETATM 13 CT 2 -3.996 2.922 1.581<br>HETATM 14 HC 2 -2.902 2.862 1.545<br>HETATM 15 HC 2 -4.281 3.703 0.865<br>HETATM 16 CT 2 0.394 2.242 -0.557<br>
HETATM 17 HC 2 -0.485 2.486 -1.167<br>HETATM 18 HC 2 1.250 2.252 -1.242<br>HETATM 19 CT 2 5.188 1.805 -2.247<br>HETATM 20 HC 2 6.018 1.286 -2.742<br>
HETATM 21 HC 2 4.300 1.615 -2.864<br>HETATM 22 CT 2 -4.587 1.582 1.127<br>HETATM 23 HC 2 -5.682 1.638 1.161<br>HETATM 24 HC 2 -4.298 0.792 1.828<br>
HETATM 25 CT 2 0.235 0.836 0.028<br>HETATM 26 HC 2 -0.616 0.818 0.720<br>HETATM 27 HC 2 1.117 0.581 0.625<br>HETATM 28 CT 2 4.981 1.206 -0.852<br>
HETATM 29 HC 2 4.152 1.720 -0.350<br><br>Jacob Harvey<br><br><div class="gmail_quote">On Sat, Apr 4, 2009 at 2:29 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Jacob Harvey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
<br>
I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following:<br>
<br>
opls_557 14.00670 ; N1 in imidazole<br>
opls_558 12.01100 ; C2 in imidazole<br>
opls_559 14.00670 ; N3 in imidazole<br>
opls_560 12.01100 ; C4 in imidazole<br>
opls_561 12.01100 ; C5 in imidazole<br>
opls_562 1.00800 ; H1 in imidazole<br>
opls_563 1.00800 ; H2 in imidazole<br>
opls_564 1.00800 ; H4 in imidazole<br>
opls_565 1.00800 ; H5 in imidazole<br>
<br>
But there are no parameters for these atoms in the ffoplsaa.rtp file. Does anyone know how I can go about naming these atoms in my pdb file? Thank you in advance.<br>
<br>
</blockquote>
<br></div>
Not every compound is present in a .rtp file. Check out its contents and you'll see what it has - pretty much just amino acids. The charges on each atom are not specific to an atom type, they are specific to a chemical species for which the parameterization scheme has been conducted. Lennard-Jones parameters are specified in ffoplsaanb.itp.<br>
<br>
I suggest a thorough read of Chapter 5 of the manual to understand the contents of these database-type files, and how they are used in assembling a topology.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Jacob Harvey<br>
<br>
-- <br>
--<br>
Jacob Harvey<br>
<br>
Graduate Student<br>
<br>
University of Massachusetts Amherst<br>
<br>
</div><a href="mailto:j.harv8@gmail.com" target="_blank">j.harv8@gmail.com</a> <mailto:<a href="mailto:j.harv8@gmail.com" target="_blank">j.harv8@gmail.com</a>><br>
<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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</blockquote></div><br><br clear="all"><br>-- <br>--<br>Jacob Harvey<br><br>Graduate Student<br><br>University of Massachusetts Amherst<br><br><a href="mailto:j.harv8@gmail.com">j.harv8@gmail.com</a><br>