Hi,
sorry for responding that late. The problem in the end was that first in
specbonds the search length was 0.1nm off so it appeared for this structure as
if the file wasn’t used but it was. and second i had the merge the PDB chain
since there was a TER between the hetero atom and the protein r
The definition seems fine. In the pdb2gmx standard output, you should check
that directory is the one being opened.
If it is, please do a "ls ${GMXLIB}" and check the output, if the file is
there (and not inside the ff directory). Even though I am guessing this is
just a typo problem, and you are
On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote:
> Dear list,
>
> I have my own force field working folder so I cloned the entire top folder to
> no mess with the original files. I added residues to the residue type file to
> add my residues to the protein group. My FF is included due to
thanks for the answer. in the console i wrote:
GMXLIB="~/GROMACS/gromacs_ff/“
export GMXLIB
the shell is GNU bash, version 4.1.2(1)-release
Max
> On Oct 2, 2015, at 9:22 AM, João M. Damas wrote:
>
> How are you defining the GMXLIB variable in your script? Please give us
> some more informat
How are you defining the GMXLIB variable in your script? Please give us
some more information (inputs and outputs) for us to be able to help you.
João
On Thu, Oct 1, 2015 at 9:21 PM, Ebert Maximilian
wrote:
> Dear list,
>
> I have my own force field working folder so I cloned the entire top fol
Dear list,
I have my own force field working folder so I cloned the entire top folder to
no mess with the original files. I added residues to the residue type file to
add my residues to the protein group. My FF is included due to the GMXLIB
environmental variable but my modified residuestype.da
