[gmx-users] about the bond connection between different groups

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 22 22:35:51 CEST 2009 


He, Yang wrote:
> Hi Tsjerk,
> 
> Thank you very much for your introduction about how to merge two
> moleculetypes. I just follow your instructions as listed below;
> 
> I have two moleculetypes named DNA and ICE. This is what I include in
> topology file:
> 
> 
> #include "dna.itp" #include "ICE.itp"
> 

Depending on the contents of these two molecules, they may not be necessary.
The merged topology, in theory, is a combination of these two moleculetype
definitions.

> [ moleculetype ]
> 
> ; molname            cylind
> 
> DNA+ICE              1
> 
> [ atoms ] ;   nr  type resnr   res  atom  cgnr    charge      mass 1    bA
> 1   DNA    bA     1      0     178.0 ...
> 
> 20    lA     1   ICE    lA    20      0     134.0
> 
> [ angles ] ... [ dihedrals ] ... [ system ] ; Name CGMD
> 
> [ molecules ] ; Compound      #mols DNA+ICE         1
> 
> I have 19 atoms in DNA and only one atom in ICE.
> 
> Also, I have consider adding the angles and dihedrals involved in the
> interaction. Then, I also include individual itp file for the DNA and ICE
> ,respectively .
> 
> In addition , I want to freeze the atom in ICE and that is what I include in
> .mdp file :
> 
> energygrp_excl          = ICE ICE
> 
> ;       Non-equilibrium MD ; freezegrps              =ICE freezedim
> = Y Y Y
> 
> [ system ] ; Name CGMD
> 
> [ molecules ] ; Compound      #mols DNA+ICE         1
> 
> But when I run this, it shows that: "Group ICE not found in indexfile. Maybe
> you have non-default goups in your mdp file, while not using the '-n' option
> of grompp. In that case use the '-n' option."
> 
> Can you tell me what is the problem? Thank you for your suggestions.
> 

You have defined a molecule called "DNA+ICE" so you need to use an index group 
to decompose its components into those that you wish to use.

-Justin

> Regards,
> 
> Yang
> 
> ___________________________________ From: gmx-users-bounces at gromacs.org
> [gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
> [tsjerkw at gmail.com] Sent: Wednesday, April 22, 2009 11:53 AM To: Discussion
> list for GROMACS users Subject: Re: [gmx-users] about the bond connection
> between different groups
> 
> You have:
> 
> [ moleculetype ] A [atoms] 1 ... N
> 
> and
> 
> [ moleculetype ] B [atoms] 1 ... M
> 
> and want to make a bond between atom X of A and Y of B. So you have to merge
> A and B into:
> 
> [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M
> 
> with a.o.:
> 
> [bonds] X Y+N type bond-parameters.
> 
> I hope this is clear enough. If it isn't, read Chapter 5 of the manual 
> thoroughly.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Wed, Apr 22, 2009 at 5:30 PM, He, Yang <yang.he at mavs.uta.edu> wrote:
>> Hi Tsjerk,
>> 
>> Thank you for your reply. SO you mean I can just define the bond in one
>> moleculetype.As what you said, I have to renumber all atoms from one of the
>> moleculetypes, starting at N+1, with N being the number of the last atom of
>> the first moleculetype .Then I wonder  which molecule type the atom N+1
>> belongs to . Also, I wonder how to define the new atom N+1's moleculetype
>> in the gro file . I just am not sure about that. Can you give me much more
>> information about that?
>> 
>> Thank you very much.
>> 
>> Yang ________________________________________ From:
>> gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of
>> Tsjerk Wassenaar [tsjerkw at gmail.com] Sent: Tuesday, April 21, 2009 11:22 PM
>>  To: jalemkul at vt.edu; Discussion list for GROMACS users Subject: Re:
>> [gmx-users] about the bond connection between different groups
>> 
>> Hi He Yang, Justin,
>> 
>>>> You have said bonds between distinct molecules require a merged
>>>> topology. Is there any introduction in the manual or Do you have any
>>>> example about the merged topology?
>>>> 
>>> A merged topology contains multiple moleculetype definitions in one 
>>> topol.top. Discussions are in the archives.
>> Bonds can only be defined within moleculetypes, not between them. So you'll
>> need to combine moleculetypes to create a bond between groups. For this you
>> have to renumber all atoms from one of the moleculetypes, starting at N+1,
>> with N being the number of the last atom of the first moleculetype. You
>> also have to renumber the indices for all other blocks ([bonds], [angles],
>> etc...). Then combine the blocks and finally add the new bond. If it is a
>> proper bond, you should also consider adding the angles and dihedrals
>> involved in the interaction. Note again, merging to create a bond does not
>> mean adding multiple moleculetypes in one topol.top!
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR,
>> Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The
>> Netherlands P: +31-30-2539931 F: +31-30-2537623 
>> _______________________________________________ gmx-users mailing list
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> 
> 
> 
> -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet
> Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P:
> +31-30-2539931 F: +31-30-2537623 
> _______________________________________________ gmx-users mailing list
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
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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