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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 18 03:35:07 CEST 2011

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? 


> 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 

> 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.



> 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
> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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