Hello,<br><br>In an earlier message, it was stated that topolbuild generated topologies with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the only files in the "dat/gromacs" directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-AA force field used?<br>
<br>Thank you.<br><br>Nancy<br><br><br><br><br><div class="gmail_quote">On Mon, Aug 10, 2009 at 6:22 PM, Bruce D. Ray <span dir="ltr"><<a href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</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><div style="font-family: tahoma,new york,times,serif; font-size: 10pt;"><div><div></div><div class="h5">On <font face="Tahoma" size="2">Sunday, August 9, 2009 at 4:32:19 PM, </font><font face="Tahoma" size="2">Nancy <<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a>> wrote:<br>
</font><br><span style="font-family: times new roman,new york,times,serif;">> I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:<br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"></span><a style="font-family: times new roman,new york,times,serif;" rel="nofollow" href="http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb" target="_blank">http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb</a><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">>
</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF<br>
</span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">Chimera (</span><a style="font-family: times new roman,new york,times,serif;" rel="nofollow" href="http://www.cgl.ucsf.edu/chimera/" target="_blank">http://www.cgl.ucsf.edu/chimera/</a><span style="font-family: times new roman,new york,times,serif;">).</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the topologies:</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">$ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir .../topolbuild1_2_2/dat/gromacs -ff gmx53a6</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">which outputs the files:</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">ethanediol.gro</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">ethanediol.log</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">ethanediolMOL.mol2</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">ethanediol.top</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">ffethanediol.itp</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">posreethanediol.itp</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">I modified the "ffethanediol.itp" file to read:</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">=======================================</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">
#define _FF_GROMOS96</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">#define _FF_GROMOS53A6</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">#define _FF_USER</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">[ defaults ]</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"> 1 1 no 1.0 1.0</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">
#include "ffG53a6nb.itp"</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">=======================================</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">The
lack of hydrogen bonds between the solute and solvent molecules was<br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">due
to the lack of charges in the generated topology file
"ethanediol.top". <br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">So I changed the "atoms" section of the topology
file (the original topology<br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">file is at the end of this message), and
this causes hydrogen bonds between the<br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">solute and solvent in numbers
comparable to that between the solvent molecules.</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">=======================================</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">[ atoms ]</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">; nr type resnr residu atom cgnr charge mass</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"> 1 CH2 1 EDO C1 1 0.17600 14.02700 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"> 2 OA 1 EDO O1 1 -0.5740 15.99940 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">
3 H 1 EDO HO1 1 0.39800 1.00800 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"> 4 CH2 1 EDO C2 2 0.17600 14.02700 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;"> 5 OA 1 EDO O2 2 -0.5740 15.99940 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">
6 H 1 EDO HO2 2 0.39800 1.00800 ; 0.0000000</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">; total molecule charge = 0.0000000</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">=======================================</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">> </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">I
obtained the charge values from the methanol tutoral included with
Gromacs<br></span><span style="font-family: times new roman,new york,times,serif;">> </span><span style="font-family: times new roman,new york,times,serif;">(.../share/gromacs/tutor/methanol/methanol.itp). I then
enlarge the box and solvate the molecule:</span><br style="font-family: times new roman,new york,times,serif;"><br style="font-family: times new roman,new york,times,serif;"></div></div><span style="font-family: times new roman,new york,times,serif;">I used a mol2 file that I generated from a sy2 file downloaded from NCI </span><span style="font-family: times new roman,new york,times,serif;">by first</span><br>
<span style="font-family: times new roman,new york,times,serif;">running the file through dos2unix then replacing the 0 in the residue number<br>column with 1 EDO so that I had both a correct residue number column with a<br>
residue name column. The NCI data was missing the residue name column. I then<br>read the mol2 file that resulted into UCSF Chimera and used it to generate gasteiger<br>charges for ethylene glycol. Chimera wrote the following mol2 file as a result:<br>
<br><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">@<TRIPOS>MOLECULE</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">EDO</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">10 9 1 0 0</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">SMALL</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">AMBER99</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">@<TRIPOS>ATOM</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 1 O1 0.0000 0.0000 0.0000 O.3 1 EDO -0.3940</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO 0.0662</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 3 C2 -1.7400 1.1400 -1.1400 C.3 1 EDO 0.0662</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 4 O2 -2.5200 1.2800 0.0200 O.3 1 EDO -0.3940</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 5 H1 0.5196
-0.8024 0.0879 H 1 EDO 0.2102</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO 0.0588</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO 0.0588</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 8 H4 -2.3721 1.1133 -2.0029 H 1 EDO 0.0588</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 9 H5 -1.0696 1.9696 -1.2252 H 1 EDO 0.0588</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 10 H6 -3.0271 2.0935 -0.0316 H 1 EDO 0.2102</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">@<TRIPOS>BOND</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 1 1 5 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 2 1 2 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 3 2 7 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 4 2 6 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 5 2 3 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 6 3 9 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 7 3 8 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 8 3 4 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 9 4 10 1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
<span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">@<TRIPOS>SUBSTRUCTURE</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> 1
EDO 2 RESIDUE 4 A EDO 0 ROOT</span><br><br style="font-family: times new roman,new york,times,serif;"></span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">I processed this with topolbuild 1.3 and generated topologies with gromacs</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">53a6 and with opls-aa as the force fields. I am attaching the results to this<br>as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa atom<br>
types selected by topolbuld 1.3 have characteristic atom type charges charges<br>of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,<br>+0.06 for each of the
hydrogens bound to carbon, and +0.145 for each of the<br>carbons. The comparison to the gasteiger charges Chimera assigned to these<br>atoms is interesting. The opls-aa topology generated also assigns to the<br>O1-C1-C2-O2 dihedral </span><span style="font-family: times new roman,new york,times,serif;">the diol constants found as a special define in<br>
</span><span style="font-family: times new roman,new york,times,serif;">ffoplsaabon.itp<br><br style="font-family: times new roman,new york,times,serif;"></span><span style="font-family: times new roman,new york,times,serif;"></span><span style="font-family: times new roman,new york,times,serif;"></span><span style="font-family: times new roman,new york,times,serif;">{snipped}<br>
</span><div class="im"><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">> The ethylene glycol lacks explicit non-polar hydrogens; is that
normal for this type of system,<br>> force field (based on GROMOS96 53a6)
and SPC/E water model?</span><br style="font-family: times new roman,new york,times,serif;"><br></div><span style="font-family: times new roman,new york,times,serif;">The 53a6 force field is a united atoms model force field and incorporates non-polar<br>
hydrogens in the parameters of the carbons to which they are bound. If you want<br>to treat the non-polar hydrogens separately from the carbons to which they are<br>bound, you will need to use an all atoms force field such as opls-aa for which I<br>
have included the parameters in the attached </span><span style="font-family: times new roman,new york,times,serif;">tarred and gzipped file, ethanediol.tgz</span><br><br><span style="font-family: times new roman,new york,times,serif;">I hope this is useful.</span><br>
<br><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">-- </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">Bruce D. Ray, Ph.D.</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">Associate Scientist</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">IUPUI</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">Physics Dept.</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">402 N. Blackford St.</span><br style="font-family: times new roman,new york,times,serif;">
<span style="font-family: times new roman,new york,times,serif;">Indianapolis, IN 46202-3273</span><div><br></div></div><br>
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