[gmx-users] pdb2gmx with DNA
Justin A. Lemkul
jalemkul at vt.edu
Sun Jul 11 00:11:35 CEST 2010
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.
Patargias, George wrote:
> 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
> 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?
>> Thanks a lot
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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