Thank you!
Sincerely yours,
C Kim
---------- Forwarded message ----------
From: *Tree* <[email protected] <mailto:[email protected]>>
Date: Wed, Mar 4, 2009 at 10:11 AM
Subject: Re: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Dear Justin:
On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Tree wrote:
Dear Justin:
Thank you for your answer!!
Yes, I found there is already a bond defined for CT and CT,
meanwhile I am waiting response from gmx-uses. I deleted mine!
To confirm, I cannot avoid to ask you a question again.
So, please let me explain...
Sections [ bonds ], [pairs], [angles] and etc. in the
"topol.top" show the information on what interaction (and how)
exist among atoms in those sections.
Real potential values are interpreted (assigned) when I run
"grompp" to get "tpr" file.
--- Is this right?
Yes.
If this is right, I do not understand why I am not able to have
new "topol_new.top" file when I use "-pp topol_new.top" with
"grompp".
There is no error message...
It isn't produced?
It is produced.
However, it seems having ALL the informations from '.atp', 'bon.itp' and
'nb.itp'...
Since I guessed that I would get a "processed" topology file having
information, which was blank in the original topology file, this looks
pretty weird...
--- What does the "-pp" option generate when doing grompp-?
The -pp option gives you a "processed" topology, explicitly showing
every parameter that grompp assembled.
Yes... That is what I understood...
Since I do not think I had an appropriate "processed" topology, I
guessed that there may be different meaning.
Thank you for your confirmation.
Regarding the assignment of opls_xxx to atom type is, I think,
well described in the file, "csoplsaanb.itp".
Is that some sort of modified form of ffoplsaanb.itp? Often times a
more detailed explanation is found in the .atp file for the
corresponding force field.
-Justin
Thank you again!
Sincerely
C Kim
On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
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 <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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
========================================
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