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Hi!
when I run "packmol-memgen --pdb 1bl8.pdb --lipids DOPE:DOPG --ratio 3:1 --keepligs", followed error thrown.
Traceback (most recent call last):
File "/root/anaconda3/bin/packmol-memgen", lin…
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I would like to set multiple positional restraints with openmm. There has been support for this type of application in AMBER under the Group Specification portion of the AMBER in files ([http://archiv…
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I want to decompose the energies of a system by atom, but am puzzled by the outputs. I'm using commands of the form
energy test1 @2 out test1.txt
energy test2 @1-10 out test2.txt
with the trpzi…
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Implementation of the pH exchange.
"In pH-REMD, although the manipulation of mdin file is kind of trivial, there's actually an additional input file called cpin file which needs to be generated us…
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### Documentation Link
_No response_
### Problem
Hello everyone
I am currently running a MD and I am calculating the energy from the trajectory using MMPBSA and it works normally, but now that …
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See, for example: https://travis-ci.org/slochower/smirnoff-host-guest-manuscript/jobs/533433413#L2248
(One thing I am confused about is why this error pops up intermittently when the citation shoul…
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We should figure out whether we want YANK to depend on `ambermini` (which is based on an older version of AmberTools) or the latest `ambertools` (which we will need to copy to `omnia` to the `ambermd`…
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### Comment:
Just as an FYI: release candidates for AmberTools24 will be coming soon (late March, 2024). My general recommendation is that people here wait for the second or third candidate (early Ap…
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Hi everyone,
I'm using OpenMM as part of a workflow that uses Amber .prmtop and .inpcrd files as inputs. I've noticed that when I use PDBReporter or PDBFile.writeFile to write out simulation states…
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Attached are VMD views of my protein after completing step 4 of the tutorial and visualizing the pdb + prmtop file.
I used VMD to select the center lipids, identified their resids, and then used the …