Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 4 23:50:03 CET 2009
Tree wrote:
> 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-?
Replace each #include statement with the text of the file that it calls.
> 2) Is it right if the "processed" topology has *ALL* of the
> information from oplsaa.rtp and opls*.itp.
>
There should be no information from the .rtp, but yes, the entirety of
ffoplsaa.itp (with the nb.itp and bon.itp) should be present.
As long as grompp does not report errors, then each of your specifications
(bonds, angles, atom types, etc) are present under the force field. The
processed topology is just an explicit confirmation of these parameters all in
one file.
-Justin
> Thank you!
>
>
> Sincerely yours,
>
> C Kim
>
> ---------- Forwarded message ----------
> From: *Tree* <tree.csc at gmail.com <mailto:tree.csc at 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 at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
>
> Dear Justin:
>
>
>
> On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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 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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> <mailto:gmx-users at gromacs.org>
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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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