Using Waterswap for the first time?

[abbas khan]

Hi Everyone,

I have successfully installed Sire. I want to know how to use it. I have installed it on a separate folder and my .top and .crd files are in another folder. I want to know whether I need to move it to the sire folder or not?

Can I use it on GPU or not?

I am a beginner.

Thanks, everyone!  

[Christopher Woods]

  Hi,

The instructions to run waterswap are here;

http://siremol.org/pages/apps/waterswap.html

Assuming you have installed Sire in $HOME/sire.app then you can run a waterswap calculation using the command

$HOME/sire.app/bin/waterswap -c /path/to/file.crd -t /path/to/file.top -l LIG

where /path/to/file is the full path to the input file, and LIG is the name of one residue in the ligand you want to swap.

Waterswap comes with more help via

$HOME/sire.app/bin/waterswap —help

and

$HOME/sire.app/bin/waterswap —help-config

More instructions are also available in he workshop here

<https://ccpbiosim.github.io/xswaps_workshop/>

You can download the jupyter notebooks in that workshop and run them using the jupyter that comes within Sire.

While Sire does have GPU support, e.g. via SOMD, this cannot be used by waterswap. This is because the Monte Carlo algorithm used by waterswap does not parallelise well on a GPU. It is better to use a many-core computer, e.g. a 16+ core Xeon server.

You don’t need to move any files into the sire.app folder (and in general you shouldn’t move files like that as you should keep software separate from you input files and results of computational experiments).

  Best wishes,

  Christopher

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[abbas khan]

Thank you for your reply. I use the same methodlology but it is showing the following error

[clsdqw-abbas@mu07 ~]$ $HOME/sire.app/bin/waterswap -c md2.mdcrd -t com_solvated.top -| *

-bash: 1lyd.pdb: command not found

usage: waterswap [-h] [--description] [-H] [--author] [--version]

                 [-l [LIGAND]] [-t [TOPOLOGY_FILE]] [-c [COORDINATE_FILE]]

                 [-C [CONFIG]]

                 [--lambda_values LAMBDA_VALUES [LAMBDA_VALUES ...]]

                 [-n [NUM_ITERATIONS]] [-f]

waterswap: error: unrecognized arguments: -

Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>

BrokenPipeError: [Errno 32] Broken pipe

[clsdqw-abbas@mu07 ~]$ sire.app/bin/waterswap -c md2.mdcrd -t com_solvated.top -| *

-bash: 1lyd.pdb: command not found

usage: waterswap [-h] [--description] [-H] [--author] [--version]

                 [-l [LIGAND]] [-t [TOPOLOGY_FILE]] [-c [COORDINATE_FILE]]

                 [-C [CONFIG]]

                 [--lambda_values LAMBDA_VALUES [LAMBDA_VALUES ...]]

                 [-n [NUM_ITERATIONS]] [-f]

waterswap: error: unrecognized arguments: -

Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>

BrokenPipeError: [Errno 32] Broken pipe

[abbas khan]

-----------------------------------

Best Regrads,

ABBAS KHAN,

Laboratory of Structural Bioinformatics,

State Key Lab of Microbial Metabolism,

Department of Bioinformatics & Biostatistics,

School of life Sciences & Biotechnology,

Shanghai Jiaotong University, Shanghai, China,

Email: abba...@sjtu.edu.cn / abbas...@163.com

contact: 008618217291370 / 00923129656006.

--

[Christopher Woods]

It is “-l” (lowercase L) not “-|”. The error is because the “|” symbol is a shell pipe.

You need to put the name of a residue in your ligand as the next value, e.g. if your ligand had the name LIG for one of its residues, then you need “-l LIG”. It is not the name of the PDB file (not 1lyd.pdb).

  Best wishes,

  Christopher

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[abbas khan]

Thank you very much. now showing the following error.

-----------------------------------

Best Regards,

ABBAS KHAN,

Laboratory of Structural Bioinformatics,

State Key Lab of Microbial Metabolism,

Department of Bioinformatics & Biostatistics,

School of Life Sciences & Biotechnology,

Shanghai Jiaotong University, Shanghai, China,

Email: abba...@sjtu.edu.cn / abbas...@163.com

contact: 008618217291370 / 00923129656006.

[Christopher Woods]

The argument to "-l" should be the name of one of the residues in the ligand you want to swap. You cannot use "*" as this is a shell wildcard character that will add every filename in your current directory to the command line.

Your command needs to be;

cd $HOME/piperine_simulation/simulations/compound-3

$HOME/sire.app/bin/waterswap -c md2.mdcrd -t com_solvated.top -l LIG

(assuming that "LIG" is the name of one of the residues in your ligand)

  Best wishes,

  Christopher

---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com

[abbas khan]

this '*" is the ligand actually.

-----------------------------------

Best Regrads,

ABBAS KHAN,

Laboratory of Structural Bioinformatics,

State Key Lab of Microbial Metabolism,

Department of Bioinformatics & Biostatistics,

School of life Sciences & Biotechnology,

Shanghai Jiaotong University, Shanghai, China,

Email: abba...@sjtu.edu.cn / abbas...@163.com

contact: 008618217291370 / 00923129656006.

[Christopher Woods]

Then use

cd $HOME/piperine_simulation/simulations/compound-3

$HOME/sire.app/bin/waterswap -c md2.mdcrd -t com_solvated.top -l "*"

You need to put the * in quotes as it is a special shell character so will get interpreted by the shell before being passed into waterswap. Ideally you should not name ligands using special shell characters as it will make analysis and running programs difficult. I generally recommend naming your ligand something simple like "LIG"

  Best wishes,

  Christopher

[biotechuos4]

Thank you very much for yout help.

Sent from my Samsung Galaxy smartphone.

[biotechuos4]

Can we run it on multiple CPUs and how?

Sent from my Samsung Galaxy smartphone.

-------- Original message --------

From: Christopher Woods <chrys...@gmail.com>

Date: 22/02/2019 2:12 pm (GMT+05:00)

To: sire-...@googlegroups.com

Subject: Re: [sire-users] Re: Using Waterswap for the first time?

[Christopher Woods]

waterswap will automatically use all of the CPUs available on your computer. To control the number of threads, use the "--ppn" option, e.g.

waterswap --ppn 16 

will tell the program to use 16 threads (if you have 16 cores).

Waterswap can only parallelise over the CPUs in a single node. You cannot run waterswap over multiple nodes in a cluster.

  Best wishes,

  Christopher

[abbas khan]

now showing this error.

Traceback (most recent call last):

  File "/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/pkgs/sire-2018.2.0/share/Sire/scripts/waterswap.py", line 199, in <module>

    WSRC.run(params)

  File "/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner

    retval = func()

  File "/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/lib/python3.5/site-packages/Sire/Tools/WSRC.py", line 2905, in run

    (wsrc_system, wsrc_moves) = loadWSRC()

  File "/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/lib/python3.5/site-packages/Sire/Tools/WSRC.py", line 2712, in loadWSRC

    proteinsys = createSystem(protein_topfile.val, protein_crdfile.val, proteinsys_scheme)

  File "/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/lib/python3.5/site-packages/Sire/Tools/AmberLoader.py", line 394, in createSystem

    system = MoleculeParser.read(top_file,crd_file)

UserWarning: Exception 'SireError::io_error' thrown by the thread 'master:main'.

There is not enough information in this parser (AmberPrm( title() = 'complex-3', nMolecules() = 15777, nResidues() = 106504, nAtoms() = 55179 )) to start the creation of a new System. You need to use a more detailed input file.

Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireIO/moleculeparser.cpp, LINE: 1445, FUNCTION: virtual SireSystem::System SireIO::MoleculeParser::startSystem(const QVector<QString>&, const SireBase::PropertyMap&) const

__Backtrace__

(  0) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireError.so.2018 ([0x2ab8ae344c7e] ++0x2e)

  -- SireError::getBackTrace()

(  1) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireError.so.2018 ([0x2ab8ae341a16] ++0x86)

  -- SireError::exception::exception(QString, QString)

/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireIO.so.2018(+0x1fa7d2) [0x2ab8a94b97d2]

(  3) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireIO.so.2018 ([0x2ab8a94ed5fd] ++0x14d)

  -- SireIO::MoleculeParser::startSystem(QVector<QString> const&, SireBase::PropertyMap const&) const

(  4) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireIO.so.2018 ([0x2ab8a94f93e2] ++0x132)

  -- SireIO::MoleculeParser::toSystem(SireIO::MoleculeParser const&, SireBase::PropertyMap const&) const

(  5) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libSireIO.so.2018 ([0x2ab8a94f96da] ++0x19a)

  -- SireIO::MoleculeParser::read(QString const&, QString const&, SireBase::PropertyMap const&)

/lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/lib/python3.5/site-packages/Sire/IO/_IO.so(+0x101a3c) [0x2ab8c134ea3c]

(  7) /lustre/home/acct-clsdqw/clsdqw-abbas/sire.app/bin/../lib/libboost_python.so ([0x2ab8aa00713d] ++0x30d)

"complex.err" 93L, 6404C   

-----------------------------------

Best Regrads,

ABBAS KHAN,

Laboratory of Structural Bioinformatics,

State Key Lab of Microbial Metabolism,

Department of Bioinformatics & Biostatistics,

School of life Sciences & Biotechnology,

Shanghai Jiaotong University, Shanghai, China,

Email: abba...@sjtu.edu.cn / abbas...@163.com

contact: 008618217291370 / 00923129656006.

[Christopher Woods]

  Hi,

The error shows that there is something wrong with the topology file you are using to run the simulation. To debug this more, could you run the attached script (also copied below in case this does not survive transmission via email).

==== test_file ====

import sys

from Sire.IO import MoleculeParser

s = MoleculeParser.read(sys.argv[1])

print(s)

===============

Run this as "$HOME/sire.app/bin/python test_file com_solvated.top"

and then send us the output.

To work, waterswap needs to start from a well-equilibrated protein-ligand system that is solvated in a cubic periodic box of water. How did you create your input files? Did you add a TIP3P cubic box of water? Did you run minimisation and equilibration using e.g. sander or pmemd? If not, you may want to check out the BioSimSpace project which can help you set up simulation inputs ready for free energy calculations. You can find the BioSimSpace project at https://biosimspace.org

  Best wishes,

  Christopher

[abbas khan]

this is the output after running that file.

-----------------------------------

Best Regrads,

ABBAS KHAN,

Laboratory of Structural Bioinformatics,

State Key Lab of Microbial Metabolism,

Department of Bioinformatics & Biostatistics,

School of life Sciences & Biotechnology,

Shanghai Jiaotong University, Shanghai, China,

Email: abba...@sjtu.edu.cn / abbas...@163.com

contact: 008618217291370 / 00923129656006.

[Christopher Woods]

The error "No such file or directory" means that the Python is not able to find the "test_file" file in the directory in which you ran the command.

The "test_file" file that I emailed is a python script, and from your response I guess that you have little experience writing or running python scripts?

Waterswap, like many computational chemistry programs, depends on knowing the basics of running and writing short python programs. To make progress, I think you need to spend a little time learning how to write and run basic python programs. There are many tutorials available. Here is the one that we use at Bristol;

<https://chryswoods.com/beginning_python>

(I am biased as I wrote it!)

Please could you spend a few days working through this workshop. You can go at your own pace and I am happy to answer questions. Once you have finished this workshop you will then have the skills needed to understand how to run the "test_file" script that I emailed to you.

  Best wishes,

  Christopher