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Hello,
I would like to use parmed to retrieve the bond information of a system containing a protein and a ligand.
I would like to provide the psf, pdb and top and par files required, and generate…
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When I run intermol with https://github.com/dspoel/liquid-simulations/blob/master/FF/GROMACS/CGenFF/TOP/GAS/1-butanol.top as input I get:
type input(gromacs) output (lammps) …
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Originally identified in #164 but I didn't realize what the problem was at the time. This didn't occur in openmm7.4.2 but does in the current available version of openmm7.5. I haven't tested openmm7.6…
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FATAL ERROR: redistrib lone pair forces: no Lphost exists for LP 15891
My ligand have lone pairs. I set the "lonepairs on" in the .conf file and it run smooth however sometimes it give the above er…
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GROMACS tools fails to include .itp files necessary for topologies generated by CHARMM-GUI. .itp files need to manually pasted into a single .top file for tool to run. Is it possible for this tool to …
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It seems that sometimes it returns a very large number for the xyz coordinates
```
(htocsp) [qzhu8@str-i2 calc]$ head xafpay02-g149-p284*.crd
* NONE *
* DATE: 8/23/24 13: 6:10 CREATE…
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Hello,
my name is Alexander Vogel and I'm trying to add a new simulation with 3 runs (7 microseconds each) to the databank (DOIs: 10.5281/zenodo.10635871 - 10.5281/zenodo.10635875 - 10.5281/zenodo.…
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I am trying to use Gromacs top and gro files to create charmm prm file using [this ](https://github.com/ParmEd/ParmEd/issues/305#issuecomment-293444294)post's code. However, I am getting errors. Here …
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Issue for myself to remind me that we need to add support for CMAP terms and chamber files (and the CHARMM forcefield generally) to the AmberPrm parser.
This will be particularly important as use o…
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Currently when an incorrect pdb file name is passed to `read_pdb` an `IOError` is thrown, e.g., `IOError: [Errno 2] No such file or directory: './output/run2.pd'`. This provides helpful output to a u…