Since I cannot see my message on the gmx-users mail list, I am forwarding this again.<div>I am sorry to bother your email box again...</div><div><br></div><div>Hope you would understand...<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Tree</b> <span dir="ltr"><<a href="mailto:tree.csc@gmail.com">tree.csc@gmail.com</a>></span><br>Date: Fri, Mar 13, 2009 at 8:51 PM<br>Subject: Matching atom name and types in OPLS-aa FF<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Cc: Chansoo Kim <<a href="mailto:tree.csc@gmail.com">tree.csc@gmail.com</a>><br><br><br><span style="border-collapse:collapse">Dear All:<br>
<br><br>I appreciate your answer always.<br><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>
<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><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><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><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>
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>
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>
<br>To summarize my question, how the assignment between opls_xxx and name in the "bon.itp" can be defined-?<br><br>I hope my question and Englsh are clear enough...<br><br>Thank you again!<br><br><br>Sincerely,<br>
<font color="#888888"><br>Kim</font></span>
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