Violated angle constraints in OPLS isopropanol
- Jirsak
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8 years 7 months ago #55
by Jirsak
Dear community,
I have an issue with a UA OPLS model of 2-propanol. The molecule gets weirdly deformed in simulation, in a way that clearly violates the fixed angles setting in .mcf.
A folder with all the files is here:
owncloud.cesnet.cz/public.php?service=fi...a7fc69fb4744bfb8b80e
I used a configuration with only single molecule to make a minimal example. Note, that HX is just a dummy site with no interaction used to define dihedral angle.
I strictly followed the tutorial to generate the files, starting from .cml file. Do I make some stupid mistake or there is a bug in Cassandra?
Thank you,
Jan
I have an issue with a UA OPLS model of 2-propanol. The molecule gets weirdly deformed in simulation, in a way that clearly violates the fixed angles setting in .mcf.
A folder with all the files is here:
owncloud.cesnet.cz/public.php?service=fi...a7fc69fb4744bfb8b80e
I used a configuration with only single molecule to make a minimal example. Note, that HX is just a dummy site with no interaction used to define dihedral angle.
I strictly followed the tutorial to generate the files, starting from .cml file. Do I make some stupid mistake or there is a bug in Cassandra?
Thank you,
Jan
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- ryangmullen
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8 years 7 months ago #56
by ryangmullen
Hi Jan,
The library_setup.py script that is bundled with Cassandra 1.0 does not handle rigid fragments. You can create the fragment file manually OR we will be posting Cassandra 1.1 for download later today. The library_setup.py script bundled with Cassandra 1.1 will transfer the coordinates for a rigid fragment from a configuration file (.pdb or .cml) to a fragment file (.dat).
FYI, Cassandra does not enforce rigid bonds or angles (i.e., it will not throw an error if your starting .pdb places two atoms 1 Angstrom apart but your .mcf file specifies a fixed bond between them of 2 Angstroms), but if a fragment is marked as rigid Cassandra will only use the configuration supplied in the .dat fragment file.
--Ryan
The library_setup.py script that is bundled with Cassandra 1.0 does not handle rigid fragments. You can create the fragment file manually OR we will be posting Cassandra 1.1 for download later today. The library_setup.py script bundled with Cassandra 1.1 will transfer the coordinates for a rigid fragment from a configuration file (.pdb or .cml) to a fragment file (.dat).
FYI, Cassandra does not enforce rigid bonds or angles (i.e., it will not throw an error if your starting .pdb places two atoms 1 Angstrom apart but your .mcf file specifies a fixed bond between them of 2 Angstroms), but if a fragment is marked as rigid Cassandra will only use the configuration supplied in the .dat fragment file.
--Ryan
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8 years 6 months ago #65
by Jirsak
Thank you for your response. Nevertheless, with Cassandra 1.1 situation is even worse - molecule "explodes". See the link for all the files:
owncloud.cesnet.cz/public.php?service=fi...a1e3ca955b7e437fe34b
owncloud.cesnet.cz/public.php?service=fi...a1e3ca955b7e437fe34b
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