cespos
cespos
Hi! I have tried to use the `databases` module but it is still not available. Is the new MMseqs version not released yet or have you decided to not add...
Thanks for your reply. Yeah, sometimes I would need to use Mg2+... But it's okay if it is not possible to have this feature. One can always prepare the system...
Hi @lohedges, Hi @jmichel80 I was able to reproduce the error with the calcium ion. See the figure below. I am also attaching here the test pdb file so that...
Hi @lohedges, sorry for taking so long to reply. Usually the TER indicates the terminal protein residue. So, if you have multiple chains, you will have a TER at the...
About the PBRadii parameter, it was more of a curiosity. This is only relevant when a Generalized Born model is used (igb != 0 in amber). I think that expert...
Thanks @lohedges for looking into this. You are right, unfortunately there is not a unique way to write PDB files. With I colleague of mine we also saw that some...
@lohedges Great to hear that you are already working on these points! I will check for future updates. Many thanks
Great, thanks!
Hi @lohedges, Sorry I saw this only now. I will test this functionality asap and let you know how it works for me. Still [feature-disulphide](https://github.com/michellab/BioSimSpace/tree/feature-disulphide) branch, right? Many thanks!
The rule is usually to have a solvent group and a solute group to avoid the "hot solvent/cold solute" problem. There are a number of references that talk about this...