[gmx-users] .top file for DNA-CNT

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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

========================================