Thanks Justin for your guidance. By following your tips, I have now all the parameters I need... Please let me know if I am missing any [ angletypes ] or [ dihedraltypes ] for a hydrocarbon molecule.<br><br>Best,<br><br>[ bondtypes ]<br>
; i j func b0 kb<br> CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file<br> CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file<br><br>[ angletypes ]<br>;i j k func th0 cth<br>
CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file<br>CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file<br>HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file<br>
<br>[ dihedraltypes ]<br> CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; hydrocarbon all-atom<br> CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom<br>
HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon *new* 11/99<br><br><br><br><br><br><div class="gmail_quote">On 30 July 2011 07:40, 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 class="im"><br>
<br>
Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello to all,<br>
<br>
I am looking for bonded and nonbonded parameters for C H atoms in saturated hydrocarbons.<br>
<br>
atom types are:<br>
Carbon atoms opls_135 opls_136 H opls_140 <br>
opls_135 12.01100 ; alkane CH3<br>
opls_136 12.01100 ; alkane CH2<br>
opls_140 1.00800 ; alkane H.<br>
<br>
Please help me out with the following:<br>
<br>
- I am wondering if I am selecting the correct values, for C-C and C-H bonds from ffoplsaabon.itp.<br>
<br>
</blockquote>
<br></div>
The C-C bond is not correct for alkanes. It is for the C-C bond of oxalic acid, as the comment indicates. In ffnonbonded.itp, you can see how opls_* types are mapped to different bonded atom types (for instance, opls_135/136 are CT). Note that in the topology, you do not have to explicitly define values when using OPLS-AA; any bond between two defined bonded atom types will be automatically detected and used.<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;">
C C 1 0.15100 292880.0 ; wlj oxalic acid, etc.<br>
HC C 1 0.10900 284512.0 ; wlj 7/96<br>
<br>
- what does wlj mean?<br>
<br>
</blockquote>
<br></div>
Probably someone's initials, which occur frequently to indicate either the source of the parameters or the individual that added them. In this case, my guess would be Jorgensen is the referenced individual here.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
- what are the units?<br>
<br>
</blockquote>
<br>
This is in the manual.<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>
Angle<br>
<br>
CA CA CZ 1 120.000 585.760 ; wlj<br>
CA CA CR 1 120.000 527.184 ;<br>
CA CA CX 1 120.000 711.280 ;<br>
C CT Cl 1 109.800 577.392 ; wlj<br>
<br>
- I can not distinguish CA CZ .... What are they referring to?<br>
<br>
</blockquote>
<br></div>
See the above tip about converting atom types in ffnonbonded.itp.<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;">
[ dihedraltypes ]<br>
<br>
C C CT HC 3 0.17782 0.53346 0.00000 -0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000)<br>
<br>
- Is this what I need for oplsaa 135 136 140?<br>
<br>
</blockquote>
<br></div>
Probably not. The comment indicates the dihedral is for dicarbonyls. The appropriate dihedral is:<br>
<br>
CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom<br>
<br>
Note how the comment indicates it is for use with hydrocarbons. Again, like bonds as described above, you do not need to explicitly list parameters in the topology. They will be inferred from the atom types.<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;">
ffoplsaanb.itp.<br>
<br>
opls_135 CT 6 12.01100 -0.180 A 3.50000e-01 2.76144e-01<br>
opls_136 CT 6 12.01100 -0.120 A 3.50000e-01 2.76144e-01<br>
<br>
opls_140 HC 1 1.00800 0.060 A 2.50000e-01 1.25520e-01<br>
<br>
- are these parameters for<br>
<br>
opls_135 12.01100 ; alkane CH3<br>
opls_136 12.01100 ; alkane CH2<br>
opls_140 1.00800 ; alkane H.<br>
<br>
?<br>
<br>
</blockquote>
<br></div>
Yes.<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;">
Also in usr/local/gromacs/share/<u></u>gromacs/top/ directory I can not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous versions these files were accessible. I am using itp files from version 4.0.7 and wanted to make sure the above parameters for oplsa_135 oplsa_136 and oplsa_140 have been remained unchanged in 4.5.4. Where can I find these files?<br>
<br>
</blockquote>
<br></div>
The force field organization has changed, but the content of the force fields has not. This is described in the manual. All the equivalent files are now in the oplsaa.ff subdirectory. For backwards compatibility, the statement #include "ffoplsaa.itp" will indeed call the force field, because you will note that ffoplsaa.itp now simply calls the correct force field with #include "oplsaa.ff/forcefield.itp."<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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