[gmx-users] Fwd: How to define "stretch" in ffoplsaabon.itp ?

[Tree]

In the section [3], the file is "csoplsaanb.itp". In the file, I found how
an opls_xxx is assigned to an atom type.
(If this is a CORRECT approach...)

Thank you!

Sincerely,

C. Kim

---------- Forwarded message ----------
From: Tree <tree.csc at gmail.com>
Date: Wed, Mar 4, 2009 at 9:38 AM
Subject: How to define "stretch" in ffoplsaabon.itp ?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Dear All:

*[1 - Situation]*
I am trying to define "stretch" between two bonded atoms (for example, in my
system PE (polyethylene), C-C).

*[2 - ffoplsaa.rtp file]*
In ffoplsaa.rtp file, I assigned
   C1    >     opls_136
   C2    >     opls_135
This can be done by my own idea, so it does not bother anything.
And totally okay.

*[3 - opls_xxx and atom type]*
I found that the oplsaa interpret those "opls_xxx" atoms to atom types
(which are in ffoplsaabon.itp file) as follows,
   opls_136     >     CT
   opls_135     >     CT.

( from a file containing
 opls_136   CT  6     12.01100    -0.120       A    3.50000e-01  2.76144e-01
 opls_137   CT  6     12.01100    -0.060       A    3.50000e-01  2.76144e-01
)

*[4 - ffoplsaabon.itp]*
Based on the information in the section [2] and [3] above, I added following
two sentences in the ffoplsaabon.itp file.

   [ bondtypes ]
   ; i    j  func       b0          kb
     CT    CT      1    0.14900   334720.0   ;

*[5 - pdb2gmx result]*
Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for
my PE system.
After that, when I looked at the topology file (e.g. topol.top), I could not
find any information in the [ bonds ] section (after the [ atoms ] section).
In other words, topol.top shows nothing in [ bonds ] section.
     [ bonds ]
     ;  ai    aj funct            c0            c1            c2
 c3
         1     2     1

*[6 - Question!]*
I think my mistake came from section [3] or [4].
   (1) Would you please let me know what I did wrong...?
   (2) If someone is familiar with defining stretch, angle, dihedral and
torsion in ffoplsaabon.itp, would you please give me an idea on how-to?
   (3) Would you please summarize how the gromacs maps opls_xxx with atom
type (C, CT... etc)?

*[7 - Thank you!]*
Thank you so much your participation and help!!!


Sincerely,

Kim
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