majid hasan wrote:
Okay, so I just removed #include forcefield from top, and [system]
[molecule] directives from the bottom of my topology file, and saved it
as .itp file. Is that fine?
Yes.
And, if I #include water topology in dna.itp file, then I shouldn't
include it in system's topology file, and it doesn't make any difference
whether I include water in a molecule.itp file or I add it explicitly in
system topology, right?
Correct. I often find it much simpler to just #include everything in one .top
file rather than having unnecessary nested #includes, but do what makes the most
sense for yourself.
Moreover, I created cnt.top using oplsaa forcefield, so in my cnt.itp
file carbon atoms' "type" is opls_240. So when I run the grompp using
amber99sb-ildn, it gives me the following error: Fatal Error: Atomtype
opls_240 not found,
which is probably because amber doesn't recognize opls_240.
Never mix and match force fields. You must have one self-consistent
representation of the system.
How should I correct the atom type in my cnt.itp file? If I just add an
atomtype opls_240 in /amber99sb-ildn.ff/atomtypes.atp, would it be
enough? Manual's section 5.8.3 says that "after definition of new atom
No. You can't simply append one force field's content to another and hope it
works. You may be able to form a syntactically correct force field, but it
would be a complete hack job that would not give anything close to a reliable
simulation.
types, additional non-bonded, and pair parameters can be defined." I
earlier added some CNT parameters ([bond types], [angle types], ..) in
ffoplsaabon.itp, do I need to make exactly the same changes in
amber.ff/ffbonded.itp?
Leave these files alone. There is no need to alter them in this case.
Is it generally not possible to create topology of one molecule using
one forcefield, and then do MD simulation of entire system using another
forcefield (without changing parameters etc.)?
In general, no, force fields cannot be combined in this way. There are limited
exceptions, but this case is not one of them. You need to choose a parent force
field that is suitable for all components of your system and derive molecule
topologies from this force field. Mixing and matching will be a great way to
waste time.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
Thanks for your help,
Majid
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Sun, April 17, 2011 4:54:11 PM
*Subject:* Re: [gmx-users] .top file for DNA-CNT
majid hasan wrote:
> Dear All,
>
> I want to simulate DNA-CNT interaction, and reproduce the helical
wrapping of DNA around CNT in the first step, and later study the
effects of temperature, CNT length etc on the favorable geometries of
hybrid.
>
> I have created .top files for DNA, and CNT separately. To generate
the top file of entire system (DNA-CNT), I added CNT in a box with DNA
using genbox. But when I try to create .top file using pdb2gmx and Amber
forcefield, I get an error that atom C in residue 11 C not found in rtp
entry because rtp because .rtp file in Amber only contain dna residues,
and if I use some other forcefield like oplsaa then dna residues won't
be present. So how do I create the .top file for whole system i.e DNA-CNT?
>
> Mailing list suggests that another and probably easier way of doing
this is to create .itp file for CNT, and add it to dna.top file using
#include file mechanism. So I wanted to ask how can I create .itp file
from topology file (because I have the toplogy file for CNT), or do I
need to create it manually from scratch?
>
The conversion of .top to .itp is simple. A .top is a system topology
and contains a description of the entire system. An .itp file describes
one type of molecule. To create a .itp from a .top, follow this:
http://www.gromacs.org/Documentation/File_Formats/.itp_File
Then a simple system topology is just:
#include (whatever force field)
#include "cnt.itp"
#include "dna.itp"
#include "spc.itp" (or whatever water)
#include "ions.itp" (if needed)
Finish with appropriate [system] and [molecules] directives.
-Justin
> Thank You,
> Majid
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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