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I set the harness generator as the README guided and worked on `7z` with it. I found a question on START_FUNCTION in the process, as I didn't find any info about start_function in `drltrace.PID.log`, …
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## Is your feature request related to a problem? ##
If I want to use MDAnalysis when I use desmond as the MD engine I have to convert it to some other format and then read that other format.
## De…
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When I try to convert a Desmond .cms file to any other format I get the following error:
Traceback (most recent call last):
File "convert.py", line 811, in
main()
File "convert.py", lin…
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Hi All,
I have a system consisting of a protein-ligand complex in 150 mM NaCl solvent. When I run MD on this system using Desmond, everything runs smoothly. When I try to use convert.py using Int…
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Hello,
I would like to know under which settings the DesmondDMSFile reader will give similar energies to those obtained by desmond.
I tested opls2005 with pme in both desmond and openmm but it seems…
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Hello,
I am trying to work with prmtop generated using Intermol from a desmond cms file (2018-4 opls2005). I tried to do energy minimization using amber but it will fail:
[desmond_setup_2-out.cms…
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I would like to know how to make the conversion DESMOND-->AMBER.
From here, it is tell that the conversion will be DESMOND--> GROMACS --> AMBER.
Using the command:
`python convert.py --des_in…
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Hi,
I was trying to use intermol to convert my Desmond cms file to gromacs. The cms file (linked) was created with the OPLS_2005 force field, water type TIP3P, using Maestro2016-4. It's a small prot…
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Good work so far. However you still need to make a few changes.
- Kindly try to align the sections in the mobile version of your portfolio. You can use flex-box property to achieve this.
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I believe [this line](https://github.com/shirtsgroup/InterMol/blob/develop/intermol/desmond/desmond_parser.py#L514) contains a typo because `ivdwtypes` is never defined (only `ivdwtype`). If this is t…
ctk3b updated
7 years ago