<p>Dear Dr. Periole:</p>
<p><br>Thank you for your answer.</p>
<p>You meant that the types of potential functions do not have any relations with OPLS-aa (except first ("1") case).<br>Those (from "2"...) are defined as written the Gromacs manual.</p>
<p><br>Thank you again.</p>
<p><br>Sincerely,</p>
<p>Kim<br><br></p>
<div class="gmail_quote">On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br>On Mar 16, 2009, at 9:34 AM, tree wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear Justin and All:<br><br><br>I truly appreciate your clear answer.<br>Since my questions are solved by your explanations, I do not know how I can express my grateful heart.<br>
<br>Now I have to ask second step questions. :)<br>It is related to the OPLS-aa "bon.itp" file.<br>Each section (bonds, angle, diherdal, and etc.) has its "type".<br>I am wondering if this "type" (of course, in OPLS-aa case) has the same meaning in the Gromos potentials.<br>
As we know, those types for each kind of bonded interactions are well described in the Gromacs manual with clear equations.<br>So, my question is (as I mentioned just above) if this is the same as the OPLS-aa case.<br></blockquote>
</div>Yes, the bond, angle, dihedral types are independent to the underlying force field<br>and correspond to the description in the manual.
<div>
<div></div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>To make my question clear, I want to give an example.<br><br>[ bonds ]<br>...<br>CT HC 1 0.10900 284512.0 ; CHARMM 22 paramter<br>
...<br><br>I know the number "1" here means type, which describes what kind of the bonds (strech) between two bonds is used.<br>If this is Gromos potential, I am sure this "1" means "harmonic" potential according to the Chap. 4 of the Gromacs manual.<br>
Is this also applied to OPLS-aa FF?<br><br>Thank you for your care, again.<br><br><br>Sincerely yours,<br><br>Kim<br><br>On Fri, 13 Mar 2009, Justin A. Lemkul wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Tree wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear All:<br>I appreciate your answer always.<br>Right now, I am trying to add/modify some values in OPLS-aa FF.<br>
I am confused atom type (opls_xxx) and atom name (e.g., C) in "atp", "bon.itp", and "nb.itp" files.<br>Please let me try the situation by an example, first.<br>In "atp" file,<br> ...<br>
opls_058 12.01100 ; C in COOR ester JPC3315(91)<br> opls_059 15.99940 ; O= in COOR ester<br> ...<br>In "bon.itp" file,<br> ...<br> C CA 1 0.14900 334720.0 ; wlj 8/97<br> C_2 CA 1 0.14900 334720.0 ; wlj 8/97<br>
...<br>In "nb.itp" file,<br> ...<br> opls_009 C2 7 14.02700 0.000 A 3.90500e-01 4.93712e-01 ; SIG<br> opls_010 C3 6 15.03500 0.000 A 3.90500e-01 7.32200e-01 ; SIG<br> ...<br>
I hope you can sense what my question is here.<br>When I define a residue in "rtp" file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx.<br>Then, gromacs (pdb2gmx) is using "rtp" file to assign each atom to the opls_xxx.<br>
"nb.itp" also has opls_xxx information inside, so I can understand how those values are assigned.<br>However, I am not clear how the procedue assign bonded potentials to the system, because "bon.itp" file does not have any information related to the opls_xxx.<br>
</blockquote><br>It does, but only indirectly. Example, from ffoplsaa.rtp:<br><br>[ ACE ]<br>[ atoms ]<br> CH3 opls_135 -0.180 1<br>HH31 opls_140 0.060 1<br><br>From ffoplsaanb.itp:<br><br>opls_135 CT 6 12.01100 -0.180 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>So the more literal interpretation of opls_135 is atom type CT, and opls_140 is HC. I assume this is done for convenience.<br><br>Therefore, in ffoplsaabon.itp:<br>
<br>CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my "pdb" file. (I doubt this... If this question is true, it can't be used for general cases.)<br>
</blockquote><br>Nothing is typically done based on atom names; atom types are much more important when considering bonded and non-bonded potentials.<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">This is subsequently how I can add new values in the "bon.itp" file by assigning the name in an appropriate way...<br>
I think I am relatively clear in assigning between opls_xxx and name in "nb.itp" file.<br>To summarize my question, how the assignment between opls_xxx and name in the "bon.itp" can be defined-?<br></blockquote>
<br><br>Translate the opls_XXX atom types to a more "literal" type given in ffoplsaanb.itp.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I hope my question and Englsh are clear enough...<br>Thank you again!<br>Sincerely,<br>Kim<br><br>------------------------------------------------------------------------<br>
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Graduate Research Assistant<br>ICTAS Doctoral Scholar<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>
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</blockquote><br></div></div></blockquote></div><br>