[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Fri Jun 20 00:09:22 CEST 2014

On 6/19/14, 3:00 PM, Matthew Stancea wrote:
> (Ignore the earlier message)
>>>> Ah, because it's Amber.  Amber force fields are special and have specific
>   nomenclature that signifies N- and C-termini, so they automatically get built.
>   Changing the residue names by removing the N and C prefixes should fix things.
>>> Okay, which file do I remove the N and C prefixes from?
>> Coordinate file, always manipulate the coordinate file.
>> But the fact that you're asking this tells me that likely you never actually
> added those prefixes, so pdb2gmx is being "smart" and adding them for you.  In
> that case, there's nothing you can do short of (1) modifying the pdb2gmx code,
> (2) manually hacking the topology - ugly, but effective, or (3) using a
> different force field that doesn't have terminus-specific naming (anything
> that's not Amber).
> After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2).
> Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select "none" for the termini), I received this error message:
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 4.6.2
> Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Does this have to do with the fact that I did select "none" for both terminals both of the times?

Yes, because pdb2gmx has difficulty figuring out that your termini have full 
valences on each of the atoms in the peptide bond.  Special bonds and .rtp bonds 
are handled separately.

If your input structure has all of the necessary hydrogen atoms (named 
correctly), then you *might* be able to get away with using the -missing flag. 
This is not something that is normally recommended, and it is potentially 
dangerous.  Any topology generated with -missing should be scrutinized heavily 
to make sure everything is right.  I can only think of one other constructive 
use of -missing, so be advised (and this goes for anyone else who comes across 
this post) that this is generally a very bad idea, so don't try to apply it in 
any other case.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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