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License: Apache License 2.0
I am setting up systems to run RBFE calculations, so a protein+ligand system and a ligand-only system. In the ".top" files of both systems I include both 'ffMOL2.itp', with the atom types and vdW parameters of the ligand (incl. dummy atoms), and 'merged.itp', with merged parameters of the hybrid ligand.
However, when using the Solvate block, everything runs correctly but the output .zip file of the ligand-only system, with all the necessary files for the topology, does not include 'merged.itp', while for the protein+ligand system it is included in the .zip normally. Looking at the logs of the ligand-only solvate run, 'merged.itp' is correctly unzipped from the input .zip topology, but in the end to zip everything back it is not detected at all, not even as a file to ignore, like the ff or the water .itp. It looks like it is not detected at all by the relevant biobb_common.tools methods.
I include the input files and code (.ipynb) to reproduce.
$conda list
# packages in environment at /home/francho.nerin-fonz/miniforge3/envs/biobb_wf_pmx_tutorial:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
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ambertools 23.3 py310hc095264_3 conda-forge
amberutils 21.0 pypi_0 pypi
anyio 4.4.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge
arpack 3.8.0 nompi_h0baa96a_101 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
binutils 2.40 h4852527_7 conda-forge
binutils_impl_linux-64 2.40 ha1999f0_7 conda-forge
binutils_linux-64 2.40 hb3c18ed_0 conda-forge
biobb_analysis 4.2.0 pyhdfd78af_0 bioconda
biobb_common 4.2.0 pyhdfd78af_0 bioconda
biobb_gromacs 4.2.0 pyhdfd78af_0 bioconda
biobb_pdb_tools 4.2.0 pyhdfd78af_0 bioconda
biobb_pmx 4.2.1 pyhdfd78af_0 bioconda
biopython 1.84 py310hc51659f_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.6 hef167b5_0 conda-forge
boost 1.78.0 py310hcb52e73_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.3 h4bc722e_0 conda-forge
c-compiler 1.7.0 hd590300_1 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
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cffi 1.16.0 py310h2fee648_0 conda-forge
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lerc 4.0.0 h27087fc_0 conda-forge
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libblas 3.9.0 23_linux64_openblas conda-forge
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packmol 20.15.0 hc8b2c43_0 conda-forge
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perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
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platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
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pmx_biobb 4.1.3 py310he3a19b2_0 bioconda
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python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytraj 2.0.6 pypi_0 pypi
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pyyaml 6.0.1 py310h2372a71_1 conda-forge
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qhull 2020.2 h434a139_5 conda-forge
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requests 2.32.3 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.19.1 py310h42e942d_0 conda-forge
sander 22.0 pypi_0 pypi
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send2trash 1.8.3 pyh0d859eb_0 conda-forge
setuptools 71.0.4 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlalchemy 2.0.31 py310hc51659f_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tenacity 9.0.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
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types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
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tzdata 2024a h0c530f3_0 conda-forge
unicodedata2 15.1.0 py310h2372a71_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
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websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
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xz 5.2.6 h166bdaf_0 conda-forge
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gmx genrestr bb is now typically used to overwrite an already existing position restraint file, because it is already included in the GROMACS topology file as ifdef. Example:
; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_C.itp"
#endif
Could we explore the possibility to have a new bb or an extension of this one, able to modify the topology with the new protein restraint itp files inside?
Hi Dough,
This is an example of a Docker call of Gmx Select using a selection with two named groups (“Mynewgroup” and "Protein-H”). It has been tested without success in the Gromacs docker images 2018.4 and 2020.2
docker run -v $(pwd):/inout gromacs/gromacs:latest /bin/bash -c "gmx -nobackup -nocopyright select -s /inout/make_ndx.tpr -on /inout/output_ndx.ndx -select ' "Mynewgroup" group "Protein-H" and not same residue as within 0.4 of resname ARG\’ "
Regards,
Pau Andrio
<make_ndx.tpr>
if input_solvent_gro_path file is not used, check the solvent property where the gromacs defaults can be selected
Hi,
I've recently updated to 3.9 and it seems that now everything is run inside a temporary sandbox dir while previously only the .zip topology file was decompressed inside a temporary folder.
So now, if I want to restart a run from a checkpoint file I get this error:
Program: gmx mdrun, version 2022
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 192)
Function: void gmx::{anonymous}::throwBecauseOfMissingOutputFiles(const char*, gmx::ArrayRef<const gmx_file_position_t>, int, const t_filenm*, size_t)
Inconsistency in user input:
Some output files listed in the checkpoint file
/home/pbarletta/labo/22/locuaz/e458d803-2586-4812-adfa-810796b54b4b/npt_nb.cpt
are not present or not named as the output files by the current program:)
Expected output files that are present:
Expected output files that are not present or named differently:
/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.log
/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.xtc
/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.edr
That is, since the temporary dir (faf79796-f8fe-4f8b-8647-2bd6f6d90226
) always changes, I can't properly restart an MD.
Am I getting this right or is there something else going on? Because this would be quite an issue for most workflows, I assume.
Please try to integrate the gmx insert-molecules tool, to be able to generate Mixed Solvent MD boxes.
gmx_select has an optional input named input_ndx_path. The functionality of this bb is exactly the one of the GROMACS select tool: it produces a new index file (ndx) with (only) the newly generated group. It would be really good if the output ndx file could contain not only the new group, but all the groups defined in the input ndx file + the new group (append).
In biobb_gromacs.make_ndx, the string mask (e.g. echo -e 'a D*\n0 & ! 19\nname 20 FREEZE\nq') is not properly read.
Testing the same tutorial in version 3.6 / 3.7 (with biobb_md instead of biobb_gromacs) runs properly.
Can be something related with the new biobb_common?
The concentration property, should have 0 as default value instead of 0.05.
Pre-configured mdp files in the gromacs.grompp and gromacs.grompp_mdrun building blocks should be changed by the official GROMACS mdp files from the official MD setup tutorial:
https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/-/tree/main/data/input
Hi,
I'm trying to conda install and I get the following error:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:|@/linux-64::__glibc==2.35=0
Your installed version is: 2.35
My os is Ubuntu 22.04.1
I've already got biobb_common installed.
Also, does this try to conda install gromacs? Can I use my own existing install?
Thank you,
Dan
gmx genion bb needs a new optional input: input_ndx_path, to be able to use custom groups where to add the ions (e.g. second water shell). Besides, a new property should be included, enabling group selection (now hardcoded to SOL).
Currently the las GROMACS version for MacOS is 2019.1 and the last version for linux 2020.4. So we decided to stay in 2019.1 in both for now.
We should check with the GROMACS/conda team when the conda package for MacOS will be updated.
grompp (and grompp + mdrun) wrapper/s should use the official mdp files from the gromacs tutorials:
https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/-/tree/main/data/input
They have separated mdp files for amber and charmm, min, nvt, npt and md (free).
Hello,
I am trying to run MD using the quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0
docker with GPU settings on a machine with 4 GPUS, but it crashes with the following error:
Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.
I would be grateful for any insight you can provide.
Thank you,
Nazanin
Hi!
I find myself needing the -box
option on editconf
*, but given that the -d
flag is not optional, my -box
dimensions get overwritten by it, even if I set -d
to 0
or a negative value.
So, would it be possible to remove the default value here, and instead of adding it eagerly here just add something like:
if self.distance_to_molecule:
self.cmd.append("-d " + str(self.distance_to_molecule))
fu.log("Distance of the box to molecule: %6.2f" % self.distance_to_molecule, self.out_log, self.global_log)
I know this would leave the door open for someone not specifying neither -d
nor -box
, which shouldn't be allowed, right? So, perhaps what I'm asking for is to add the -box
option and make it so either one of them is set.
IDK, let me know if this makes sense, I have no problem doing this myself, it should be fairly quick.
Cheers!
*: which I'll be able to use in the next release through the new dev option (thanks!)
If "center" property is set to False, the "center_selection" property (by default "System") seems to be used anyway. As a consequence, "output_selection" is completely ignored and "center_selection" is used to determine which atoms should be dumped in the output trajectory. I guess this is because the groups are written in the following order in the .stdin: "center_selection" "output_selection". And if no centering is requested just one group is required and just the first one is used.
Maybe the easiest solution would be to avoid including the "center_selection" group in the .stdin whenever "center" is False. In that way the default value of "center_selection" would not mess with the output group.
I think grompp_mdrun is using a temporal unique folder into which "internal.tpr" is written. Instead of creating the .tpr file in the corresponding step folder. Due to this, if one needs to image the trajectory afterwards with gmx_image, the .tpr file is not found in the corresponding step folder.
Make output_trr_path optional in mdrun. Nowadays trr is almost not used.
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