francesca vitalini wrote:
Thanks Tsjerk, Florian,
However I need the .gro file for the reverse transformation and I
cannot simply obtain it through pdb2gmx as it won't recognize the
atoms
Use editconf to convert between .pdb and .gro (as well as other formats).
pdb2gmx is for producing topo
Thanks Tsjerk, Florian,
However I need the .gro file for the reverse transformation and I
cannot simply obtain it through pdb2gmx as it won't recognize the
atoms
Fatal error:
Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms
while sorting atoms.
.
Any help with that?
Thanks a l
On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote:
> Just one last question Tsjerk, I was trying to load the cg.gro file
> obtained with martinize in vmd and the program says it is unable to
> load the molecule. the result of the martinize script looks like:
>
> MODEL1
> TITLE
Hi Francesca,
The output is written in .pdb format. That's also stated in the help.
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 4:05 PM, francesca vitalini
wrote:
> Just one last question Tsjerk, I was trying to load the cg.gro file
> obtained with martinize in vmd and the program says it is unabl
Just one last question Tsjerk, I was trying to load the cg.gro file
obtained with martinize in vmd and the program says it is unable to
load the molecule. the result of the martinize script looks like:
MODEL1
TITLE Protein in water
CRYST1 29.094 29.094 29.094 90.00 90.00 90.0
Thank you so much.. Now it is working. I was trying to do it without
specifying the secondary structure as I'm having problems with the
do_dssp command. It is not working basically and I have to use pdb2gmx
to convert into pdb then go to the dssp webpage and create the dssp
file from there through
Hey Francesca,
Now there's a small bug in the program. Sorry about it. We'll put the
fixed version on in a bit. The problem arises because you don't
specify the secondary structure and pymol is not yet available for
doing so. The workaround is to explicitly set the secondary structure
to loop, by
Done while waiting for your e-mail. the error message now says
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNINGPosition re
Hi Francesca,
Given the error, it seems there's still a mismatch between the number
of atoms and the number indicated. Try converting your structure to
PDB and use that for coarsegraining.
Cheers,
Tsjerk
On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini
wrote:
> I've changed that but it is s
I've changed that but it is still complaining...
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNINGPosition restraints are o
Hi Francesca,
The problem is that the second line of your gro file indicates there
are 2410 atoms in the file, while there are only 25. Did you manually
remove water? In that case you have to update the number of atoms in
the second line. The error message should be more explanatory though.
Cheer
I was using the one available from the tutorial but now I have
downloaded the new one and it gives me still an error message like
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO
Hi Francesca,
Is this the latest version
(http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)?
If it is, please send me the input file and I'll fix the bug. Note
that the previous version that was available online was one used in a
workshop, while the script was still in beta.
Hi all,
I'm trying to coarsegrain my structure using the script martinize.py
and using my gro file as inmput and the dssp file with the second
structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the
pdb structure as input, I get the following error message that I
really don't understand
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