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

majid hasan pu_majidhasan at yahoo.com
Mon Apr 18 03:14:48 CEST 2011

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?

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.

 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 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?

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.)?

Thanks for your help,

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:


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.


> Thank You,
> Majid

-- ========================================

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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