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Sire Users

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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, Christopher3

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 Michel6

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.com3

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 Woods8

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 Woods2

5/10/20

Dear Javier, Thanks for getting back in touch. I assume everything went well with your ligandswap and

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Dear Javier, Thanks for getting back in touch. I assume everything went well with your ligandswap and

5/10/20

Faisal Ahmad, Christopher Woods3

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

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 Woods16

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.com3

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 Woods6

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 Woods6

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 Woods2

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 Woods3

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 Ocello7

3/12/18

Dear Christopher, sorry for the late reply. This is the command: $SIRE/python ../sample.py K+ AM1

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Dear Christopher, sorry for the late reply. This is the command: $SIRE/python ../sample.py K+ AM1

3/12/18

Riccardo Ocello, Christopher Woods2

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 Michel2

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 Mey23

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 Woods2

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 Woods3

9/10/17

Hi, I've looked in more detail through the code and there are a few places to look: (1) SireMM::

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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 Michel9

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 Woods2

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 Woods2

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 Woods7

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 Woods4

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 Woods2

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 Woods12

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 Michel8

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 Loeffler2

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

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