Hi Michael,
Proteins are actually very easy, because of the fixed connectivity...
I'll post a few scripts soon to coarse grain a protein in Pymol, and
to fix/show the connectivity. I'll have to combine some things from
scriptlets here and there, though.
Cheers,
Tsjerk
On Thu, Aug 18, 2011 at 9:
On Thu, Aug 18, 2011 at 3:39 AM, Tsjerk Wassenaar wrote:
> Hey :)
>
> Here is an all Python solution to load a .gro file, including the box
> vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
> It supports multimodel files. I'll probably add a mechanism to
> identify chains f
To keep the original residue numbers from the gro file, you could also
temporarily store additional numbering in the segment identifier, and
after loading get it back from there:
_pdbline= "ATOM %5i %-3s %3s%2s%4i" +\
"%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s \n"
def pdbOut(atom,i=
Hi Joseph,
Sorry about that. A bit naive with the numbering. To fix it, change the function
def pdbOut(atom,i=1):
return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
(atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
to
def pdbOut(atom,i=1):
stuff =
[i%1e5,atom[0][:3],atom[1
Hi Tsjerk,
Thanks for the script. It works great on my protein. However when I try to
load the solvated system > 100.000 atoms I have problems with water
molecules. Is it possible to handle gro files with more than 100.000 atoms
and residues?
Best
On Thu, Aug 18, 2011 at 9:39 AM, Tsjerk Wa
Hey :)
Here is an all Python solution to load a .gro file, including the box
vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
It supports multimodel files. I'll probably add a mechanism to
identify chains from breaks, as the .gro format does not use chain
identifiers, and may
Hi Michael,
PyMOL knows about gromacs files, but needs to better handle .gro
files, specifically. Currently you have to export to a PDB to read the
topology.
Please file this on the open-source tracker
(https://sourceforge.net/tracker/?group_id=4546) and I'll get to it
ASAP.
Cheers,
-- Jason
O
Maybe this can help you
http://sourceforge.net/mailarchive/message.php?msg_id=19472192
Cheers,
Marius
On Tue, Aug 16, 2011 at 2:19 AM, Michael Daily wrote:
> Hi all,
>
> Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
> know it's simple to convert them to pdb using edi
Hi all,
Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
know it's simple to convert them to pdb using editconf, but I want to load
gro files directly (as you can in vmd) because they permit higher max. atom
and residue numbers (100K vs. 10K for pdb) and permit longer resi
