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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Tsjerk Wassenaar [tsje...@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...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, April 21, 2009 11:22 PM
To: jalem...@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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
