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....@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@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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