[gmx-users] pdb2gmx with DNA

[Justin A. Lemkul]

I think there have been changes to the way pdb2gmx handles termini, perhaps 
related to the impending inclusion of the ffamber ports, but I do not know.  I 
worked with someone else with this issue, and it was solved by renaming 
residues, which seems like a terrible solution.  I guess your DNA is being 
interpreted as protein, which certainly isn't correct.

I would suggest filing a bugzilla for this; in theory, pdb2gmx should handle DNA 
and protein seamlessly, but something seems to be mishandled here.

-Justin

Patargias, George wrote:
> Hi 
> 
> Thanks, I thought so too. 
> 
> My command line is: pdb2gmx -f xxx.pdb file   The -ter flag is set to default, i.e. charged termini. 
> 
> When I use the -ter flag for interactive termini selection and I select NONE for both N- and C-ter
> the message becomes:
> 
> Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty
> Source code file: pdb2top.c, line: 887
> 
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> 
> Best 
> George
> 
> 
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Friday, July 09, 2010 8:08 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] pdb2gmx with DNA
> 
> Patargias, George wrote:
>> Thanks for your reply Justin.
>>
>> I am trying to generate a topology dor a dna structure using the charmm dna.rtp
>>
>> I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for
>> the 5' and 3' ends
>>
>> I got this error
>>
>>
>> Fatal error:
>> atom N not found in buiding block 2DG while combining tdb and rtp
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> I quess I need to change something in the .rtp and/or the .tdb files. But what?
>>
> 
> Maybe, maybe not.  It looks like pdb2gmx is trying to treat your DNA as protein.
>   What is your command line?  What are you choosing for termini?
> 
> -Justin
> 
>> Thanks a lot
>>
>> George--
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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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-- 
========================================

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

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