BuildModel 2 BuildSystem

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Compiling an IMP module out of tree

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changing the python version in IMP

Marcell Miski

25 Sep 2019 25 Sep '19

5:24 a.m.

Dear Imp-Users,

I am trying to model a complex using IMP however, I can't use the older IMP on a server. My problem is that when I try to change to using BuildSystem, my simulation fails.

I attach, the original modeling.py and the new modeling.py with the two inputs.

Can you help me how to fix this?

Best regards, Marcell Miski Ph.D. Student PPCU FIT BP HU

Attachments:

attachment.htm (text/html — 565 bytes)
topology2.txt (text/plain — 1.5 KB)
modeling.py (text/x-python — 5.5 KB)
topology.txt (text/plain — 1.4 KB)
interactions.csv (text/csv — 69 bytes)
modeling_new.py (text/x-python — 6.3 KB)
interacions2.csv (text/csv — 68 bytes)

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Ben Webb

25 Sep 25 Sep

10:32 a.m.

On 9/25/19 5:24 AM, Marcell Miski wrote: > I am trying to model a complex using IMP however, I can't use the older > IMP on a server. My problem is that when I try to change to using > BuildSystem, my simulation fails.

Can you give us a clue as to what the error might be?

Ben

-- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

Marcell Miski

10:47 a.m.

yes, I took a screenshot of the error message. It seems something about the CrossLinking doesn't work. [image: image.png]

Thanks for the fast response. Marcell Miski Ph.D. PPCU FIT BP HU

Ben Webb ben@salilab.org ezt írta (időpont: 2019. szept. 25., Sze, 19:32):

> On 9/25/19 5:24 AM, Marcell Miski wrote: > > I am trying to model a complex using IMP however, I can't use the older > > IMP on a server. My problem is that when I try to change to using > > BuildSystem, my simulation fails. > > Can you give us a clue as to what the error might be? > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >

Ben Webb

26 Sep 26 Sep

4:07 p.m.

On 9/25/19 10:47 AM, Marcell Miski wrote: > yes, I took a screenshot of the error message. It seems something about > the CrossLinking doesn't work.

You passed an incorrect value for the crosslink_restraints parameter to the IMP.pmi.macros.ReplicaExchange0 class. This should be a list of restraints, e.g. [xl2], not a single restraint, e.g. xl2.

Ben

-- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

Marcell Miski

4:17 p.m.

Thank you for the clarification saved me plenty of time. Now it works.

Best wishes, Marcell Miski PPCU FIT BP HU

Ben Webb ben@salilab.org ezt írta (időpont: 2019. szept. 27., P, 1:07):

> On 9/25/19 10:47 AM, Marcell Miski wrote: > > yes, I took a screenshot of the error message. It seems something about > > the CrossLinking doesn't work. > > You passed an incorrect value for the crosslink_restraints parameter to > the IMP.pmi.macros.ReplicaExchange0 class. This should be a list of > restraints, e.g. [xl2], not a single restraint, e.g. xl2. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >

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