[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Thu Jun 19 19:55:41 CEST 2014

>>> 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?


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