Comments (2)
Hi there,
Thanks for this. The issue is that the AMBER topology file contains CMAP records, which we don't currently support. Apologies that the message isn't a little more informative. We currently only provided high-level error messages by default, since the low-level messages from Sire, on which BioSImSpace is built, are often quite cryptic to the end user. We are working on an improved way to expose these.
If you are using Sire/BioSImSpace < 2023.0, you can get full error messages as follows:
import BioSImSpace as BSS
BSS.setVerbose(True)
system = BSS.IO.readMolecules(["system.prm7","system.rst7"])
For BioSimSpace 2023.0.0, this doesn't work in quite the same way since Sire has changed its error handling. To get the same error, you'd need to try loading the topology directly with Sire.
from sire.legacy import IO
amber_prm = AmberPrm("system.prm7")
Both report the following:
...
UserWarning: SireIO::parse_error: Could not extract the format from the line '%COMMENT Ala CMAP '. Expected to read a line similar to '%FORMAT(5E16.8)'.
CMAP records are in our roadmap of features for the next year. While it is easy enough to add read/write support for a given format, we need to do some work dealing with interoperability and making sure that the terms are preserved during molecular editing, or applied correctly for certain simulation protocols.
For now, I'll try to give the user a more informative error message when this problem occurs.
from biosimspace.
I've now parsed the error message and let the user know that CMAP records are currently unsupported. Thanks again for reporting.
from biosimspace.
Related Issues (20)
- Storage quota exceeded on the Anaconda cloud HOT 1
- HILLS file not updating during restarting simulation HOT 4
- Is it possible to add ions to an already solvated system, without adding any more water molecules? HOT 4
- Problem when converting Gro/Top to Rst7 HOT 12
- Making HMR work with dummies HOT 11
- Make _removeDummies() recognise dummy bonds HOT 10
- Would it be possible to include HiMap as an alternative to LoMap in the generateNetwork method? HOT 2
- Unable to import BioSimSpace after mamba installation HOT 12
- BioSimSpace.Align.viewMapping: py3Dmol.view not rendering in Jupyter Notebook HOT 11
- `_toRegularMolecule` failing with `convert_amber_dummies=True` HOT 15
- Absolute Binding Free Energy Calculations with GROMACS HOT 7
- Pickling a parametrised molecule from an SDF file with GAFF2 HOT 4
- Are atomtypes meant to be updated when using repartitionHydrogenMass? HOT 16
- [BUG] OSError "It looks like you failed to include a topology file." when reading SDF which doesn't contain redundant bond order information HOT 10
- [BUG] Cannot import BioSimSpace after installation of biosimspace 2023.1.2 using mamba HOT 3
- AnalysisError: SOMD free-energy analysis failed! HOT 5
- [BUG] HOT 10
- Reporting a vulnerability
- [BUG] Water molecule coordinates are setting to (0,0,0) HOT 4
- Issue in reproducing the funnel methadynamics tutorial HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from biosimspace.