[gmx-users] Re: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing your message to the list and would ask that all 
further discussion be sent there.  See comments below.

Yanping Fan, Liza (Dr) wrote:
> Dear Justin:
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> Good day.
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> 
> I found your comments in gmx-user communications. And you are very 
> experienced in GMX. I’m using gmx 453 now, with DNA system. Pdb2gmx is 
> ok, but gmx treated each string as protein. I used command
> 

What do you mean "treated each string as protein?"  DNA residues are defined in 
residuetypes.dat as such, so I don't know how DNA residues would be interpreted 
as protein by any tool.  In principle, there is no problem with this 
interpretation, as long as the parameters are assigned correctly.

The .pdb file you sent me contains both protein and DNA, so I suspect that 
nothing is wrong; you have some residues that are DNA and others that are 
protein.  You don't say which tool is treating your DNA as protein, but I would 
encourage you to check the output carefully.  If you still suspect something is 
wrong, please provide useful diagnostic information (i.e., the tool reporting 
the potential problem and the output it is giving you that leads you to suspect 
a problem).

>  
> 
> pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p
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> then choose charmm27 ff,
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> everything looks good. However I found during my md runs, DNA separated. 
> System goes to weird. Do I need to remove TER between the paired stands? 
>  I attached pdb file for your reference.  Thank you very much for your 
> guildance.
> 

There is probably not separation, just a periodicity effect.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

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> Best regards,
> 
>  
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> Liza
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> 
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-- 
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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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