Dear Dr. Periole:
Thank you for your answer. That was the point which I wanted to double check (of course after reading the manual...). Thank you again! Sincerely, Kim On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole <[email protected]> wrote: > > On Mar 17, 2009, at 8:45 AM, tree wrote: > > Dear Justin: >> >> >> Thank you for your email! >> >> Thanks to your help and explanation, I am feeling more comfortable with >> OPLS topology modification. >> Before this work, I have used Gromacs without modifying FF paramters for >> simulating 'water' in general systems, which can easily obtained from PDB >> sites. >> So, it was not too easy to generate a sort of new topology even I've >> learned MD. >> >> I understand what you meant here. :) >> I did not mean the selection "1" (Harmonic potential function) is a sort >> of OPLS-aa FF functions. >> My question is actually if I can use the Forth power potential when I >> choose "2" in bond streching section. >> 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. >> So, my question here is >> [can I use the Forth power potential for bond strech using the given >> OPLS-aa paramters?] >> > To that the answer is no! If you change the potential to describe a bond, > angle ... > the parameters will be different! Have a look a the manual chapter 4. > > I assume this would be same to others, angle, dihedral, and etc. >> >> Thank you again. >> >> >> Sincerely, >> >> Kim >> >> On Mon, 16 Mar 2009, Justin A. Lemkul wrote: >> >> >>> >>> Tree wrote: >>> >>>> Dear Dr. Periole: >>>> Thank you for your answer. >>>> You meant that the types of potential functions do not have any >>>> relations with OPLS-aa (except first ("1") case). >>>> Those (from "2"...) are defined as written the Gromacs manual. >>>> >>> >>> 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!) >>> >>> 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. >>> >>> 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. >>> >>> -Justin >>> >>> Thank you again. >>>> Sincerely, >>>> Kim >>>> On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole <[email protected]<mailto: >>>> [email protected]>> wrote: >>>> >>>> On Mar 16, 2009, at 9:34 AM, tree wrote: >>>> >>>> Dear Justin and All: >>>> >>>> I truly appreciate your clear answer. >>>> Since my questions are solved by your explanations, I do not >>>> know how I can express my grateful heart. >>>> >>>> Now I have to ask second step questions. :) >>>> It is related to the OPLS-aa "bon.itp" file. >>>> Each section (bonds, angle, diherdal, and etc.) has its "type". >>>> I am wondering if this "type" (of course, in OPLS-aa case) has >>>> the same meaning in the Gromos potentials. >>>> As we know, those types for each kind of bonded interactions are >>>> well described in the Gromacs manual with clear equations. >>>> So, my question is (as I mentioned just above) if this is the >>>> same as the OPLS-aa case. >>>> >>>> Yes, the bond, angle, dihedral types are independent to the >>>> underlying force field >>>> and correspond to the description in the manual. >>>> >>>> To make my question clear, I want to give an example. >>>> >>>> [ bonds ] >>>> ... >>>> CT HC 1 0.10900 284512.0 ; CHARMM 22 >>>> paramter >>>> ... >>>> >>>> I know the number "1" here means type, which describes what kind >>>> of the bonds (strech) between two bonds is used. >>>> If this is Gromos potential, I am sure this "1" means "harmonic" >>>> potential according to the Chap. 4 of the Gromacs manual. >>>> Is this also applied to OPLS-aa FF? >>>> >>>> Thank you for your care, again. >>>> >>>> Sincerely yours, >>>> >>>> Kim >>>> >>>> On Fri, 13 Mar 2009, Justin A. Lemkul wrote: >>>> >>>> Tree wrote: >>>> >>>> Dear All: >>>> I appreciate your answer always. >>>> Right now, I am trying to add/modify some values in >>>> OPLS-aa FF. >>>> I am confused atom type (opls_xxx) and atom name (e.g., >>>> C) in "atp", "bon.itp", and "nb.itp" files. >>>> Please let me try the situation by an example, first. >>>> In "atp" file, >>>> ... >>>> opls_058 12.01100 ; C in COOR ester JPC3315(91) >>>> opls_059 15.99940 ; O= in COOR ester >>>> ... >>>> In "bon.itp" file, >>>> ... >>>> C CA 1 0.14900 334720.0 ; wlj 8/97 >>>> C_2 CA 1 0.14900 334720.0 ; wlj 8/97 >>>> ... >>>> In "nb.itp" file, >>>> ... >>>> opls_009 C2 7 14.02700 0.000 A >>>> 3.90500e-01 4.93712e-01 ; SIG >>>> opls_010 C3 6 15.03500 0.000 A >>>> 3.90500e-01 7.32200e-01 ; SIG >>>> ... >>>> I hope you can sense what my question is here. >>>> 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. >>>> Then, gromacs (pdb2gmx) is using "rtp" file to assign >>>> each atom to the opls_xxx. >>>> "nb.itp" also has opls_xxx information inside, so I can >>>> understand how those values are assigned. >>>> 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. >>>> >>>> It does, but only indirectly. Example, from ffoplsaa.rtp: >>>> >>>> [ ACE ] >>>> [ atoms ] >>>> CH3 opls_135 -0.180 1 >>>> HH31 opls_140 0.060 1 >>>> >>>> From ffoplsaanb.itp: >>>> >>>> opls_135 CT 6 12.01100 -0.180 A 3.50000e-01 >>>> 2.76144e-01 >>>> ... >>>> opls_140 HC 1 1.00800 0.060 A 2.50000e-01 >>>> 1.25520e-01 >>>> >>>> So the more literal interpretation of opls_135 is atom type >>>> CT, and opls_140 is HC. I assume this is done for >>>> convenience. >>>> >>>> Therefore, in ffoplsaabon.itp: >>>> >>>> CT HC 1 0.10900 284512.0 ; CHARMM 22 >>>> parameter file >>>> >>>> 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.) >>>> >>>> Nothing is typically done based on atom names; atom types >>>> are much more important when considering bonded and >>>> non-bonded potentials. >>>> >>>> This is subsequently how I can add new values in the >>>> "bon.itp" file by assigning the name in an appropriate >>>> way... >>>> I think I am relatively clear in assigning between >>>> opls_xxx and name in "nb.itp" file. >>>> To summarize my question, how the assignment between >>>> opls_xxx and name in the "bon.itp" can be defined-? >>>> >>>> Translate the opls_XXX atom types to a more "literal" type >>>> given in ffoplsaanb.itp. >>>> >>>> -Justin >>>> >>>> I hope my question and Englsh are clear enough... >>>> Thank you again! >>>> Sincerely, >>>> Kim >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> <mailto:[email protected]> >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/search before posting! >>>> Please don't post (un)subscribe requests to the list. >>>> Use the www interface or send it to >>>> [email protected] >>>> <mailto:[email protected]>. >>>> Can't post? Read >>>> http://www.gromacs.org/mailing_lists/users.php >>>> >>>> -- ======================================== >>>> >>>> Justin A. Lemkul >>>> Graduate Research Assistant >>>> ICTAS Doctoral Scholar >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> <mailto:[email protected]> >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search >>>> before posting! >>>> Please don't post (un)subscribe requests to the list. Use >>>> the www interface or send it to >>>> [email protected] >>>> <mailto:[email protected]>. >>>> Can't post? Read >>>> http://www.gromacs.org/mailing_lists/users.php >>>> >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> <mailto:[email protected]> >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search >>>> before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected] >>>> <mailto:[email protected]>. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to [email protected]. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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