Refinement with DAMMIN

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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prithaghosh
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Joined: 2019.02.22 18:20

Refinement with DAMMIN

#1 Post by prithaghosh » 2019.12.04 14:48

Dear SAXIER users,

I have been using the standalone version of ATSAS. I want to refine the DAMSTART model using DAMMIN. However, if I understand correctly, DAMMIN accepts only GNOM files as an input. How can I provide the damstart.pdb as an input to the standalone DAMMIN program?

Thank you.

Regards
Pritha

prithaghosh
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Posts: 12
Joined: 2019.02.22 18:20

Re: Refinement with DAMMIN

#2 Post by prithaghosh » 2019.12.10 15:29

Dear SAXIER users,

I could troubleshoot the issue with suggestions from Dr. Al Kikhney. In order to run DAMMIN with a starting model, alongside a GNOM output file, the program should be launched in an interactive "expert" mode. Subsequently, when prompted by the program for a starting model, the DAMSTART model can be provided as an input.

Hope this helps!

Regards
Pritha

cjuark
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Joined: 2020.02.12 05:33

Re: Refinement with DAMMIN

#3 Post by cjuark » 2020.02.12 07:17

Hello,

I am currently using the most recent version of ATSAS, 3.0, and am having trouble using the expert option. When prompted for the "input data, GNOM input file", the command prompt will not accept any value I add and instead asks again such as what I am copying:

Is this a bug in the software, or am I not using a correct name or something?

Mode: <[F]>ast, |S]low, [J]ag, [K]eep,
[E]xpert ............................... < Fast >:
Log file name .......................... < .log >: to1
Input data, GNOM output file name ...... < .out >: lyz
Input data, GNOM output file name ...... < .out >:
Input data, GNOM output file name ...... < .out >:

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AL
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Re: the command prompt will not accept any value

#4 Post by AL » 2020.02.12 20:11

You should start DAMMIN in the folder where your .out file is and provide the file name, e.g. 'lyz.out'.

cjuark
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Joined: 2020.02.12 05:33

Re: Refinement with DAMMIN

#5 Post by cjuark » 2020.02.13 19:28

That worked, thank you so much!

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