Hi Justin,<br><br>So far I have been #including ffoplsaa.itp and running simulations. The reason I was after parameters is just to have a better indea on the FF parameters rather than just using them blindly, that's it :) <br>
<br>Thank you,<br><br><div class="gmail_quote">On 31 July 2011 20:03, 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;">
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>
</blockquote>
<br></div>
Seems fine to me; grompp will complain if something is missing. Is there a reason that you're trying to parse out certain parameters? It'd be far easier to just #include "oplsaa.ff/forcefield.itp" in your topology and have the entire OPLS-AA force field available to you, rather than reinventing the wheel.<br>
<br>
-Justin<br>
<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">
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><div><div></div><div class="h5">
On 30 July 2011 07:40, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Elisabeth wrote:<br>
<br>
Hello to all,<br>
<br>
I am looking for bonded and nonbonded parameters for C H atoms<br>
in saturated hydrocarbons.<br>
<br>
atom types are:<br>
Carbon atoms opls_135 opls_136 H opls_140 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<br>
and C-H bonds from ffoplsaabon.itp.<br>
<br>
<br>
The C-C bond is not correct for alkanes. It is for the C-C bond of<br>
oxalic acid, as the comment indicates. In ffnonbonded.itp, you can<br>
see how opls_* types are mapped to different bonded atom types (for<br>
instance, opls_135/136 are CT). Note that in the topology, you do<br>
not have to explicitly define values when using OPLS-AA; any bond<br>
between two defined bonded atom types will be automatically detected<br>
and used.<br>
<br>
<br>
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>
<br>
Probably someone's initials, which occur frequently to indicate<br>
either the source of the parameters or the individual that added<br>
them. In this case, my guess would be Jorgensen is the referenced<br>
individual here.<br>
<br>
- what are the units?<br>
<br>
<br>
This is in the manual.<br>
<br>
<br>
<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>
<br>
See the above tip about converting atom types in ffnonbonded.itp.<br>
<br>
<br>
[ dihedraltypes ]<br>
<br>
C C CT HC 3 0.17782 0.53346 0.00000<br>
-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>
<br>
Probably not. The comment indicates the dihedral is for<br>
dicarbonyls. The appropriate dihedral is:<br>
<br>
CT CT CT HC 3 0.62760 1.88280 0.00000<br>
-2.51040 0.00000 0.00000 ; hydrocarbon all-atom<br>
<br>
Note how the comment indicates it is for use with hydrocarbons.<br>
Again, like bonds as described above, you do not need to explicitly<br>
list parameters in the topology. They will be inferred from the<br>
atom types.<br>
<br>
<br>
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>
<br>
Yes.<br>
<br>
<br>
Also in usr/local/gromacs/share/__<u></u>gromacs/top/ directory I can<br>
not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in<br>
previous versions these files were accessible. I am using itp<br>
files from version 4.0.7 and wanted to make sure the above<br>
parameters for oplsa_135 oplsa_136 and oplsa_140 have been<br>
remained unchanged in 4.5.4. Where can I find these files?<br>
<br>
<br>
The force field organization has changed, but the content of the<br>
force fields has not. This is described in the manual. All the<br>
equivalent files are now in the oplsaa.ff subdirectory. For<br>
backwards compatibility, the statement #include "ffoplsaa.itp" will<br>
indeed call the force field, because you will note that ffoplsaa.itp<br>
now simply calls the correct force field with #include<br>
"oplsaa.ff/forcefield.itp."<br>
<br>
-Justin<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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<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>
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