[gmx-users] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 5 18:24:27 CEST 2016


Building whole capping groups has never been in scope for pdb2gmx, and
particularly not for the AMBER force fields, which use specially
parameterised charged amino acid termini (for example). IIRC there are also
some neutral capping groups in .rtp files that are usable as residues, but
pdb2gmx does not have the ability to patch them on. It seems like you need
another tool.


On Tue, 5 Apr 2016 15:27 ABEL Stephane 175950 <Stephane.ABEL at cea.fr> wrote:

> Hello again
> I have noticed that in case of the amber* forcefields (in gromacs v504)
> the aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not
> possible to construct easily a capped AA with the pdb2gmx -ter command
> without using a rtp file (and it is very painful). So does anyone have the
> modified (uptated) aminoacids.n.tdb and aminoacids.n.tdb files that
> contains the capped entries that in charmm distribution
> *This limitation was also discussed in the following thread
> http://comments.gmane.org/gmane.science.biology.gromacs.user/69523
> Thanks
> Stephane
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