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Welcome to the Sire users' mailing list. Please feel free to use this list to discuss Sire and to ask for help about using Sire (or about any problems with Sire).
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rei...@wanadoo.es
12/18/22
Problems running WaterSwap on Sire 2023.0.1
Dear users, When using Sire (installed through Anaconda on a Linux machine), I encountered some
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Problems running WaterSwap on Sire 2023.0.1
Dear users, When using Sire (installed through Anaconda on a Linux machine), I encountered some
12/18/22
John Young
,
Christopher
3
7/9/21
Use custom forces in somd-freenrg
Hi Christopher, Thanks for the reply! I understand the situation better now. I'm not quite
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Use custom forces in somd-freenrg
Hi Christopher, Thanks for the reply! I understand the situation better now. I'm not quite
7/9/21
Michael Schauperl
,
Julien Michel
6
9/2/20
Error using harmonic restratins
Hi Michael, The distance restraints keyword together with a list of specific distances could help.
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Error using harmonic restratins
Hi Michael, The distance restraints keyword together with a list of specific distances could help.
9/2/20
Michael Schauperl
, …
julie...@googlemail.com
3
8/7/20
reflection radius in somd-freenrg
Hi Michael, There are a few tricks you can use to speed up calculations. - decrease the size of the
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reflection radius in somd-freenrg
Hi Michael, There are a few tricks you can use to speed up calculations. - decrease the size of the
8/7/20
Jans Alzate Morales
, …
Christopher Woods
8
5/22/20
Error with analysis of results in ligandswap tutorial
Dear Jans, This is an error caused by the API of the energy function changing in about 2017. The QM/
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Error with analysis of results in ligandswap tutorial
Dear Jans, This is an error caused by the API of the energy function changing in about 2017. The QM/
5/22/20
Javier García Marín
,
Christopher Woods
2
5/10/20
ProteinSwap
Dear Javier, Thanks for getting back in touch. I assume everything went well with your ligandswap and
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ProteinSwap
Dear Javier, Thanks for getting back in touch. I assume everything went well with your ligandswap and
5/10/20
Faisal Ahmad
,
Christopher Woods
3
8/21/19
watersawp error
Dear Christopher Woods Thanks for sharing such a piece of important views regarding waterswap
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watersawp error
Dear Christopher Woods Thanks for sharing such a piece of important views regarding waterswap
8/21/19
Faisal Ahmad
8/21/19
waterswap error
Hi, I am Faisal from Pakistan. I am runing wateswap calculation for one of my complex. I am facing
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waterswap error
Hi, I am Faisal from Pakistan. I am runing wateswap calculation for one of my complex. I am facing
8/21/19
sun...@qulab.com
4/4/19
somd-freenrg crashes frequently
Hi, I'm having problem running some production simulation with somd-freenrg. I did follow the
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somd-freenrg crashes frequently
Hi, I'm having problem running some production simulation with somd-freenrg. I did follow the
4/4/19
abbas khan
,
Christopher Woods
16
3/2/19
Using Waterswap for the first time?
The error "No such file or directory" means that the Python is not able to find the "
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Using Waterswap for the first time?
The error "No such file or directory" means that the Python is not able to find the "
3/2/19
carmine marco Morgillo
,
julie...@googlemail.com
3
12/21/18
nvcc fatal: Value 'sm_61' is not defined for option 'gpu-architecture'
Il giorno venerdì 21 dicembre 2018 12:29:40 UTC+1, julie...@googlemail.com ha scritto: > Hi Marco,
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nvcc fatal: Value 'sm_61' is not defined for option 'gpu-architecture'
Il giorno venerdì 21 dicembre 2018 12:29:40 UTC+1, julie...@googlemail.com ha scritto: > Hi Marco,
12/21/18
Javier García Marín
, …
Christopher Woods
6
9/7/18
Problems interpreting WaterSwap Results
Dear Saad, The swap water molecules are supposed to overlap with the ligand. This is how the method
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Problems interpreting WaterSwap Results
Dear Saad, The swap water molecules are supposed to overlap with the ligand. This is how the method
9/7/18
Javier García Marín
, …
Christopher Woods
6
8/14/18
Error using LigandSwap
Hi Javier, Thanks for your patience while we investigated the problem. The issue was a small change
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Error using LigandSwap
Hi Javier, Thanks for your patience while we investigated the problem. The issue was a small change
8/14/18
Benjamin H
,
Christopher Woods
2
7/31/18
Monte Carlo tutorials failing on 2018.2
Hi Ben, Thanks for highlighting this. It looks like changes in API of Sire since 2014 have broken
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Monte Carlo tutorials failing on 2018.2
Hi Ben, Thanks for highlighting this. It looks like changes in API of Sire since 2014 have broken
7/31/18
jm1...@my.bristol.ac.uk
,
Christopher Woods
3
3/28/18
Constraint SireSystem::SpaceWrapper() is not satisfied despite having just been applied!!!
Hi Christopher, I've attached the relevent files, including the tleap file used to generate the
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Constraint SireSystem::SpaceWrapper() is not satisfied despite having just been applied!!!
Hi Christopher, I've attached the relevent files, including the tleap file used to generate the
3/28/18
Gaetano Calabrò
, …
Riccardo Ocello
7
3/12/18
Charged Ligand
Dear Christopher, sorry for the late reply. This is the command: $SIRE/python ../sample.py K+ AM1
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Charged Ligand
Dear Christopher, sorry for the late reply. This is the command: $SIRE/python ../sample.py K+ AM1
3/12/18
Riccardo Ocello
,
Christopher Woods
2
3/7/18
from CHARM36 to Amber file format
Dear Riccardo, I am afraid that quantomm currently only supports the Amber forcefields, and is not
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from CHARM36 to Amber file format
Dear Riccardo, I am afraid that quantomm currently only supports the Amber forcefields, and is not
3/7/18
inaki morao
,
Julien Michel
2
2/14/18
openbabel error when running FESetup
Hi Inaki, Sorry for the slow reply, it's been very busy lately. It looks like your error is due
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openbabel error when running FESetup
Hi Inaki, Sorry for the slow reply, it's been very busy lately. It looks like your error is due
2/14/18
Sushil
, …
Antonia Mey
23
1/29/18
RuntimeError: There is no registered Platform called "GPU"
Hi Sushil, sorry for the slow response, but I was on holiday. Based on the PMFs, MBAR does look like
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RuntimeError: There is no registered Platform called "GPU"
Hi Sushil, sorry for the slow response, but I was on holiday. Based on the PMFs, MBAR does look like
1/29/18
cwh.s...@gmail.com
,
Christopher Woods
2
9/10/17
Water in Sphere
Hi, The warning message relates to an issue with the reflection constraint being confused by some
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Water in Sphere
Hi, The warning message relates to an issue with the reflection constraint being confused by some
9/10/17
schrodinger
,
Christopher Woods
3
9/10/17
Grids
Hi, I've looked in more detail through the code and there are a few places to look: (1) SireMM::
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Grids
Hi, I've looked in more detail through the code and there are a few places to look: (1) SireMM::
9/10/17
sajid iqbal
, …
Julien Michel
9
9/7/17
Role of inter- and intra-molecular hydrogen bonding on structure
Dear Sajid, This error normally happens when there is no periodic box information in the crd file
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Role of inter- and intra-molecular hydrogen bonding on structure
Dear Sajid, This error normally happens when there is no periodic box information in the crd file
9/7/17
marawanish
,
Christopher Woods
2
7/7/17
Estimating entropy from waterswap
Dear Marawan, Thanks for getting in touch. Yes, in theory you could try to account for entropy during
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Estimating entropy from waterswap
Dear Marawan, Thanks for getting in touch. Yes, in theory you could try to account for entropy during
7/7/17
B Albert
,
Christopher Woods
2
3/5/17
waterswap failed in new version
Hi, I think that the problem is that the restart file is not an ascii format amber "rst7"
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waterswap failed in new version
Hi, I think that the problem is that the restart file is not an ascii format amber "rst7"
3/5/17
Emilio Lence Quintana
,
Christopher Woods
7
9/22/16
Problems with Waterswap 2016.1.0
Yes, putting them on curie or bc3 would be great. Cheers, Christopher On Thursday, 22 September 2016,
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Problems with Waterswap 2016.1.0
Yes, putting them on curie or bc3 would be great. Cheers, Christopher On Thursday, 22 September 2016,
9/22/16
yusras...@gmail.com
,
Christopher Woods
4
8/30/16
Interpretation of WATERSWAP results
Hi Yusra, Running for 1000 iterations should have converged the free energies, although the results
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Interpretation of WATERSWAP results
Hi Yusra, Running for 1000 iterations should have converged the free energies, although the results
8/30/16
B Albert
,
Christopher Woods
2
7/29/16
how many CPU can we use in Sire 2016 v1?
Hi Albert, A single calculation can use up to 16 cores of a node, although the latest development
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how many CPU can we use in Sire 2016 v1?
Hi Albert, A single calculation can use up to 16 cores of a node, although the latest development
7/29/16
jmro...@ujaen.es
, …
Christopher Woods
12
6/6/16
Reproducibility between versions
Good afternoon, I am not sure if I should start another thread, although I think this is related to
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Reproducibility between versions
Good afternoon, I am not sure if I should start another thread, although I think this is related to
6/6/16
sajid iqbal
, …
Julien Michel
8
5/10/16
Build a new molecule from scratch by joining the atoms in script
Dear Julien, Thank you a lot! I am able to change the the desired atoms and consequently generated
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Build a new molecule from scratch by joining the atoms in script
Dear Julien, Thank you a lot! I am able to change the the desired atoms and consequently generated
5/10/16
Hannes Loeffler
2
3/30/16
how does AtomStructureEditor::reindex() work?
Ok, looks like mol.property('connectivity') is updated but none of the terms hiding in mol.
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how does AtomStructureEditor::reindex() work?
Ok, looks like mol.property('connectivity') is updated but none of the terms hiding in mol.
3/30/16