Tree wrote:
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 ;
There is already a CT-CT bond defined in ffoplsaabon.itp:
CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file
If you don't want those parameters, make sure you comment out that line so you
know which parameters you are actually using!
*[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
It's not showing nothing. Atoms 1 and 2 are bonded together. As long as there
are parameters defined in ffoplsaabon.itp, then grompp will interpret the
topology correctly. If grompp fails, then you have identified a problem.
*[6 - Question!]*
I think my mistake came from section [3] or [4].
(1) Would you please let me know what I did wrong...?
Nothing so far that I can see (aside from potentially duplicating parameters).
(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?
How do you define "stretch"? The force constant for how much the bond length
can deviate? Otherwise, all bonded parameters are assigned by pdb2gmx as long
as all atom types are defined.
(3) Would you please summarize how the gromacs maps opls_xxx with
atom type (C, CT... etc)?
Read ffoplsaa.atp.
-Justin
*[7 - Thank you!]*
Thank you so much your participation and help!!!
Sincerely,
Kim
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--
========================================
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
========================================
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