Closed noeliaferruz closed 8 years ago
Hmm... is the PDB file available for me to test? If not, try the bare propka31 on the same file.
By the way Noelia take care with segmentgaps
(called autoSegment
now). It doesn't modify the molecule in place, it returns a modified molecule, which in your first script you are not using afterwards.
@tonigi i cannot. I'll find another molecule @stefdoerr yes yes i know. i pseudo invented the commands
"Unfortunately" other two examples i've tried worked. I'll cat the helix that is crashing and will attach it here. (tomorrow xD)
Hi Noelia, Sent you an email about this.
Hello!!
This part of the molecule also crashes. Just rename it to pdb. I bet it is something related with the maestro format, because opening it with vmd, and writing out a new structure with the same selection solves the problem.
But perhaps useful to understand what's wrong with this format.
Thanks, Noelia
it seems a problem with hydrogen names - some software uses names (or pdb format variants) which are not recognized as hydrogens. Removing them should fix the problem (until i find a general solution).
Edit: the problem is here
HETATM 5435 1HA NMA
what is the point of keeping them in the first place?
On 15 April 2016 at 22:29, Toni G notifications@github.com wrote:
it seems a problem with hydrogen names - some software uses names which are not recognized as hydrogens. Removing them should fix the problem (until i find a general solution).
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I am basically testing the most common issues the users here will likely find.
The point is that the inexperienced user needs a set of scripts to build, equilibrate and run an adaptive. Unfortunately the inexperienced user does not want to look inside these scripts and has no interest either on trying the tutorials.
I have them split the process into four scripts: 1.build.py, 2.equil.py, 3.prod.py, 4.adaptive.py. The 3rd creates the generators and the other scripts have the obvious usage.
It turns that scripts 2,3 and 4 ALWAYS work. Script 1, rarely ever does. By working I mean that don't appear errors in the command line and the output is as expected. Note that the user very often does not know what the output should look like -and has no interest in learning so either-.
So for the part regarding 1.build.py, it would be ideal if the user could provide the protein of interest -usually prepared through maestro or similar softwares that add hydrogens or caps- and the other parts and get the system. Ideally, in the future this could look like:
./1.build.py -p protein.pdb -l ligand1.pdb ligand2.pdb -m membrane.pdb -c cofactor.pdb and so on.
At the current stage 1.build.py is far from looking to work without supervision but ideally in the future would be nice if it does.
So that's why I keep the hydrogens. If proteinPrepare doesn't handle some maestro H, I will add a line right before reading protein.filter('hydrogen') in the main script so the user doesn't have to figure out what's causing the error, while in the meanwhile proteinPrepare could become more robust and accept different kind of inputs.
Thanks, Noelia
H can be useful because propKa can decide protonation of ligand-protein complexes, but im still thinking on how to best use this.
Note that in the previous error the cause was probably the NMA appearing as HETATM... try filtering that out. In the best case it is ignored.
Thanks Toni,
Do you mean with it it's ignored that you have made some changes in proteinPrepare so that NMA is ignored now? I will otherwise filter maestro caps by default in these scripts.
Thanks, Noelia
No recent changes on that. I don't think NMA is ignored: it must be removed manually. Then build with addcaps re-adds it in the ff-specific way.
Can I close this issue*? I don't think we can/should filter some residue names (like NMA) by default. Hydrogens maybe, but it was not related to this issue.
(*) actually it seems i can comment but not close the issue
ok! sure sure
Hi all,
I was trying to use proteinPrepare, I think is a nice feature and will be very useful soon. So first I did:
This builds a system as we could expect. But this doesn't:
Let me know.
Thanks Noelia