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

Steve Fiedler fiedler at umich.edu
Wed Apr 22 22:26:56 CEST 2009 

Dear Yang,

It appears that you will either need to either A) create a new index 
file using the make_ndx utility, or B) modify your existing index file.  
If you haven't done this procedure before, the first option may be the 
easiest.  A good description of make_ndx is contained in the manual as 
well as some introductory tutorials.

 -Steve

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"
>
> [ 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.
>
> 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    gmx-users at gromacs.org
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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    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
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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