[gmx-users] How to define "stretch" in ffoplsaabon.itp ?
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 4 16:04:47 CET 2009
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 <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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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