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?
--- What does the "-pp" option generate when doing grompp-?
The -pp option gives you a "processed" topology, explicitly showing every
parameter that grompp assembled.
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]>> 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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
