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SMIRFF will use improper torsions which involve a trefoil-type SMIRKS pattern. The plan is to apply these to all (three? six? Bayly thinks 6) paths which constitute an improper to avoid problems with …
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I'm trying to compile an ffxml file from two gaff mol2 files and frcmod files. It seems to be failing somewhere under the hood in the amber parser, I think the angles get read incorrectly somewhere.
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When an interaction is turned on or off in a forcefield, it would be nice to change a state variable that indicated that the forcefield has fundamentally changed. This would be used in Molecules usin…
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@jchodera - I was under the impression from what you wrote describing your initial code that an exception would be raised if parameters were missing for any of the major required force types in a mole…
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# Aim
For _testing purposes_ we should add the _M24_ water model, introduced by Shirts and Pande1.
# Background
Shirts1 introduced a range of proof-of-concept TIP3P-like water models. He changed the…
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It has come up in #941 and #815 that we do have a problem with abstracting the away the differences between topology formats because they save different information. There are in two types of problems…
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I'm running Windows XP Home and have just installed 0.9.1 on my PC and cannot use any forcefields.
I get the error "AutoOpt:could not setup forcefield"
I have run the program using the shortcut ge…
cryos updated
8 years ago
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Latest OB and Avogadro (trunk). Qt 4.4beta1.
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0xb67e5b90 (LWP 15168)]
0xb6e731f7 in memset () from /lib/libc.so.6
(gdb) bt
#0 …
cryos updated
8 years ago
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I'm running Windows XP Home and have just installed 0.9.1 on my PC and cannot use any forcefields.
I get the error "AutoOpt:could not setup forcefield"
I have run the program using the shortcut ge…
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I am working with Windows 7 and version 2.1. I have reproduced this with the my own force field files and with force field files that come standard with aten. When I select a file to open, nothing hap…