<div>Dear Dr. Periole:</div>
<div> </div>
<div> </div>
<div>Thank you for your answer.</div>
<div>That was the point which I wanted to double check (of course after reading the manual...).</div>
<div> </div>
<div>Thank you again!</div>
<div> </div>
<div> </div>
<div>Sincerely,</div>
<div> </div>
<div>Kim<br><br></div>
<div class="gmail_quote">On Tue, Mar 17, 2009 at 6:09 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 17, 2009, at 8:45 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:<br><br><br>Thank you for your email!<br><br>Thanks to your help and explanation, I am feeling more comfortable with OPLS topology modification.<br>
Before this work, I have used Gromacs without modifying FF paramters for simulating 'water' in general systems, which can easily obtained from PDB sites.<br>So, it was not too easy to generate a sort of new topology even I've learned MD.<br>
<br>I understand what you meant here. :)<br>I did not mean the selection "1" (Harmonic potential function) is a sort of OPLS-aa FF functions.<br>My question is actually if I can use the Forth power potential when I choose "2" in bond streching section.<br>
Since this funtion has different from from "1" (Harmonic potential function), I thought that it may need other paramters that may (may not) be different from the given parameters in OPLS-aa FF.<br>So, my question here is<br>
[can I use the Forth power potential for bond strech using the given<br> OPLS-aa paramters?]<br></blockquote></div>To that the answer is no! If you change the potential to describe a bond, angle ...<br>the parameters will be different! Have a look a the manual chapter 4.
<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">I assume this would be same to others, angle, dihedral, and etc.<br><br>Thank you again.<br><br><br>Sincerely,<br>
<br>Kim<br><br>On Mon, 16 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 Dr. Periole:<br>Thank you for your answer.<br>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.<br></blockquote><br>Table 5.4 defines the different types of intramolecular interactions. You should specify the proper terms based on what corresponds to the force field functional form. That is harmonic potential does not necessarily imply OPLS, but OPLS might imply that you have to use a harmonic potential (because, in fact, many force fields use a harmonic potential for bonds, not just OPLS!)<br>
<br>You should refer to the primary literature for the force field, how it was derived, and any subsequent references regarding modifications to the force field.<br><br>Another option (in addition to doing the background reading!) is to run through some tutorial material with a simple protein under OPLS to get a feel for how an OPLS topology is automatically created by pdb2gmx.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thank you again.<br>Sincerely,<br>Kim<br>On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a> <mailto:<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>>> wrote:<br>
<br> On Mar 16, 2009, at 9:34 AM, tree wrote:<br><br> Dear Justin and All:<br><br> I truly appreciate your clear answer.<br> Since my questions are solved by your explanations, I do not<br> 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<br>
the same meaning in the Gromos potentials.<br> As we know, those types for each kind of bonded interactions are<br> well described in the Gromacs manual with clear equations.<br> So, my question is (as I mentioned just above) if this is the<br>
same as the OPLS-aa case.<br><br> Yes, the bond, angle, dihedral types are independent to the<br> underlying force field<br> and correspond to the description in the manual.<br><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<br> of the bonds (strech) between two bonds is used.<br>
If this is Gromos potential, I am sure this "1" means "harmonic"<br> 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> Sincerely yours,<br><br> Kim<br><br> On Fri, 13 Mar 2009, Justin A. Lemkul wrote:<br><br> Tree wrote:<br><br> Dear All:<br> I appreciate your answer always.<br> Right now, I am trying to add/modify some values in<br>
OPLS-aa FF.<br> I am confused atom type (opls_xxx) and atom name (e.g.,<br> 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<br> for my atom in my system and assignment between that<br> specific atom name and opls_xxx.<br>
Then, gromacs (pdb2gmx) is using "rtp" file to assign<br> each atom to the opls_xxx.<br> "nb.itp" also has opls_xxx information inside, so I can<br> understand how those values are assigned.<br>
However, I am not clear how the procedue assign bonded<br> potentials to the system, because "bon.itp" file does<br> not have any information related to the opls_xxx.<br><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<br>
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<br> parameter file<br>
<br> Also, my question related to the above sentece is<br> whether the bonded potentials are assigned according to<br> the name of atom, which I defined in my "pdb" file. (I<br>
doubt this... If this question is true, it can't be used<br> for general cases.)<br><br> Nothing is typically done based on atom names; atom types<br> are much more important when considering bonded and<br>
non-bonded potentials.<br><br> This is subsequently how I can add new values in the<br> "bon.itp" file by assigning the name in an appropriate<br> way...<br> I think I am relatively clear in assigning between<br>
opls_xxx and name in "nb.itp" file.<br> To summarize my question, how the assignment between<br> opls_xxx and name in the "bon.itp" can be defined-?<br><br> Translate the opls_XXX atom types to a more "literal" type<br>
given in ffoplsaanb.itp.<br><br> -Justin<br><br> I hope my question and Englsh are clear enough...<br> Thank you again!<br> Sincerely,<br> Kim<br><br>
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</blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>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>
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</blockquote><br></div></div></blockquote></div><br>