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

majid hasan pu_majidhasan at yahoo.com
Mon Apr 18 03:45:05 CEST 2011 

Okay, thanks, I'll stick to Amber then.

Thanks again,
Majid



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Sun, April 17, 2011 6:35:07 PM
Subject: Re: [gmx-users] .top file for DNA-CNT



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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
><mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or 
>send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110417/6629e8b0/attachment.html>

More information about the gromacs.org_gmx-users mailing list