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

He, Yang yang.he at mavs.uta.edu
Wed Apr 22 22:00:00 CEST 2009 

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
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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
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