Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?
Tree
tree.csc at gmail.com
Wed Mar 4 23:42:37 CET 2009
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-?
2) Is it right if the "processed" topology has *ALL* of the information
from oplsaa.rtp and opls*.itp.
Thank you!
Sincerely yours,
C Kim
---------- Forwarded message ----------
From: Tree <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>
Dear Justin:
On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul <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>> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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