[gmx-users] pdb2gmx with DNA

[Patargias, George]

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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