Dear Justin and All :
As I mentioned below, I want to check if my processed topology (by grompp)
is right or not.
Therefore,
1) What does the processed topology file normally have inside-?
2) Is it right if the processed topology has *ALL* of the information
from oplsaa.rtp and opls*.itp.
Thank you!
Sincerely yours,
C Kim
-- Forwarded message --
From: Tree tree@gmail.com
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 gmx-users@gromacs.org
Dear Justin:
On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul jalem...@vt.edu 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 jalem...@vt.edumailto:
jalem...@vt.edu 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 A3.5e-01 2.76144e-01
opls_137 CT 6 12.01100-0.060 A3.5e-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 ]
; ij func b0 kb
CTCT 10.14900 334720.0 ;
There is already a CT-CT bond defined in ffoplsaabon.itp:
CTCT 10.15290 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 ]
; aiaj functc0c1c2
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
