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LigFlow/ScoreFlow should first search for a compound in ChemBase for parameters instead of recomputing all over again.
This is especially important for am1-bcc and even more for RESP which take a …
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It seems that Yank only accepts mol2 files as ligands, while in my case I want to use a very short peptide as a ligand for the free energy calculation. It seems that even if I specify a pdb file as li…
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Trying to solvate a small molecule from trajectories or straight from PDB files for whatever reason inputs bond orders that are greater than 3... Any idea why this might be happening? Here's a short b…
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@leeping @MSchauperl @jchodera @davidlmobley @dgasmith
I'd like to restart the discussion of semiempirical charge methods, and how we can encode them in the SMIRNOFF spec.
Currently, users have…
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Hi,
I was checking if there are any updated instructions for compiling clasp/cando in an "agnostic" linux distro, also without being root? The deb packages have been compiled with glibc 2.34, which i…
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Particularly those that contain nitrile (for the 'CY', 'NY' atom types in Amber).
Certain chains need qualifiers which dictate how the atom types are assigned. How do we implement this? This can ti…
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Uldaman Instance (as of 27/06/2014)
1) Respawn timer on nearly all Troggs, from entrance to Ironaya, is too fast.
Most all mobs (90%) respawn in 10 minutes. This is not a big problem unless you …
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Hi,
I'd like to build an explicit solvent model from amber files.
According to the tutorial in https://github.com/maccallumlab/meld/blob/master/docs/how_to/explicit_solvent.rst :
s = system.bu…
doesm updated
11 months ago
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不好意思，在这里提问。
最近在做糖基化蛋白的模拟，糖是从实验pdb结构中拿到的，但是gromacs默认不识别这些原子。
看了你的帖子。仍然很麻烦。
好像glycam的工具可以处理，但是生成了一堆文件，不知道怎么用，求大神指点，谢谢。
源文件 我传到这里了[github](https://github.com/liyigerry/gp120/tree/master/gly)
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I'm getting this error when assigning partial charges using openeye's am1bccelf1 via the openff-toolkit:
```
def gen_charges(smc):
offmol = smc.to_openff()
offmol.assign_partial_charges(…