[gmx-users] How to define "stretch" in ffoplsaabon.itp ?

[Justin A. Lemkul]

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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-- 
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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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