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

Tree tree.csc at gmail.com
Wed Mar 4 16:01:11 CET 2009 

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?

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...
--- What does the "-pp" option generate when doing grompp-?

Regarding the assignment of opls_xxx to atom type is, I think, well
described in the file, "csoplsaanb.itp".

Thank you again!


Sincerely

C Kim

On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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