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Hi Axel,
For some pdb files, I'm finding that TopoTools outputs a LAMMPS data file with a tilt factor greater than half the distance of the parallel box length, giving a LAMMPS error unless one fir…
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Dear Developers,
I'm using the TopoTools commands `clearbonds` and `addbonds` to correctly set the bonds for my system which works like a charm. However the definition of residues is not updated ba…
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Hello,
Can ParmEd convert .psf file to .top file.
Mamta
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Hello,
I want to use topotools 1.6 for topology conversion.
After download I untar the file and as instructed in install instructions, I copied directory topotools1.6/
in directory: /usr/local/lib/v…
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Hello,
I used TopoTools on a sample alanine.pdb file and generated a structure.top file.
grompp gives following error:
Program gmx grompp, VERSION 5.1.1
Source code file: /home/mamta/Gromacs/gromacs…
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I am using TopoTools 1.4 version to create a data file using VMD. For a non-orthorhombic system, the box parameters written in data file are wrong.
for eg: box -- 23.694 23.694 10.046 90 90 120
…
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Proposed new structure from claw-dev hackathon working group....
geoclaw contains
src
examples
tests
geoclaw/src contains
1d
2d
3d
python
matlab
geoclaw/src/2…