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MolSoft ICM Knowledge Base

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Welcome to MolSoft's ICM Knowledge Base. It is a forum for you to interact with the worldwide ICM-user community and keep up-to-date with the latest ICM computational biology and chemistry tools. Please feel free to ask questions, report bugs or share scripts. You can use the search bar above to search for a particular topic.

Other resources include:

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Command Line User Manual [here...]
Product Specific Manuals [here...]
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Aug 22

Including Prior Knowledge or Known Actives in GigaScreen Training

Q. Can I include prior knowledge or known actives in a GigaScreen training set? A. Yes. You can

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Including Prior Knowledge or Known Actives in GigaScreen Training

Q. Can I include prior knowledge or known actives in a GigaScreen training set? A. Yes. You can

Aug 22

Jul 29

How to use ICM command line to read and write PDB Files in ICM

Q: How do I load a PDB file into ICM? A: read pdb "1atp" More about read pdb here. Q: How

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How to use ICM command line to read and write PDB Files in ICM

Q: How do I load a PDB file into ICM? A: read pdb "1atp" More about read pdb here. Q: How

Jul 29

Jul 22

In RIDE, how can I preserve certain regions of the reference molecule while allowing other parts to vary—for example, for a scaffold-hopping application?

Q: In RIDE, how can I preserve certain regions of the reference molecule while allowing other parts

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In RIDE, how can I preserve certain regions of the reference molecule while allowing other parts to vary—for example, for a scaffold-hopping application?

Q: In RIDE, how can I preserve certain regions of the reference molecule while allowing other parts

Jul 22

Jul 16

ICM Commands for Molecular and Solvent Accessible Surfaces

Q: What does the "Receptor Pocket" visualization in ICM represent? Is it solvent accessible

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ICM Commands for Molecular and Solvent Accessible Surfaces

Q: What does the "Receptor Pocket" visualization in ICM represent? Is it solvent accessible

Jul 16

Jul 9

GPU-Accelerated Molecular Dynamics with ICM-Pro - Common Questions

With built-in OpenMM support, MolSoft ICM-Pro brings fast, GPU-accelerated molecular dynamics

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GPU-Accelerated Molecular Dynamics with ICM-Pro - Common Questions

With built-in OpenMM support, MolSoft ICM-Pro brings fast, GPU-accelerated molecular dynamics

Jul 9

Jul 7

How can I switch MolPipe tools to use the ICM-Chemist license instead of the default ICM license?

Q: How can I switch MolPipe tools to use the ICM-Chemist license instead of the default ICM license?

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How can I switch MolPipe tools to use the ICM-Chemist license instead of the default ICM license?

Q: How can I switch MolPipe tools to use the ICM-Chemist license instead of the default ICM license?

Jul 7

Jul 3

Flexlm Licensing Error - The license server manager (lmgrd) has not been started yet,

Here are some things to try if you have a flexlm floating license and you see the error reported

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Flexlm Licensing Error - The license server manager (lmgrd) has not been started yet,

Here are some things to try if you have a flexlm floating license and you see the error reported

Jul 3

Jun 28

Understanding Charge and Stereochemistry Handling in GINGER Conformer Generation

Before running GINGER to generate 3D conformers in .molt format, it's helpful to understand how

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Understanding Charge and Stereochemistry Handling in GINGER Conformer Generation

Before running GINGER to generate 3D conformers in .molt format, it's helpful to understand how

Jun 28

Jun 24

Some common questions about using restraints in ligand docking.

Some Common Questions About Using Restraints in Ligand Docking You can define hydrogen bond donor or

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Some common questions about using restraints in ligand docking.

Some Common Questions About Using Restraints in Ligand Docking You can define hydrogen bond donor or

Jun 24

Jun 5

QSAR – Descriptor Generation, Classification Models, and Diverse Selection

Q: Can ICM generate numerical descriptors for QSAR modeling? A: Yes. Go to Chemistry → Calculate

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QSAR – Descriptor Generation, Classification Models, and Diverse Selection

Q: Can ICM generate numerical descriptors for QSAR modeling? A: Yes. Go to Chemistry → Calculate

Jun 5

Jun 3

If I am interested in a subset of a .molt file, is it possible to filter the .molt file? Or would you recommend filtering the .sdf file, then generating a subset .molt file from the filtered .sdf file?

Just to clarify: The filtering example above applies to 3D conformer molts (eg, those generated by

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If I am interested in a subset of a .molt file, is it possible to filter the .molt file? Or would you recommend filtering the .sdf file, then generating a subset .molt file from the filtered .sdf file?

Just to clarify: The filtering example above applies to 3D conformer molts (eg, those generated by

Jun 3

Jun 3

GINGER - Charge and Stereochemistry Questions

Q: Do formal charge assignment and stereochemistry enumeration need to be done prior to running

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GINGER - Charge and Stereochemistry Questions

Q: Do formal charge assignment and stereochemistry enumeration need to be done prior to running

Jun 3

Jun 2

Troubleshooting NaN Errors in OpenMM

Q: I received an error saying “Particle coordinate is NaN” when running MD in ICM. What does this

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Troubleshooting NaN Errors in OpenMM

Q: I received an error saying “Particle coordinate is NaN” when running MD in ICM. What does this

Jun 2

May 31

Where do I specify how many poses to keep when batch docking a large .sdf file?

Q: Where do I specify how many poses to keep when batch docking a large .sdf file? A: You should

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Where do I specify how many poses to keep when batch docking a large .sdf file?

Q: Where do I specify how many poses to keep when batch docking a large .sdf file? A: You should

May 31

May 30

Matching SMARTS patterns of unwanted moieties to a chemical spreadsheet.

Q: Can I supply a list of ~100 SMARTS patterns (of unwanted moieties) to automatically mark/select/

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Matching SMARTS patterns of unwanted moieties to a chemical spreadsheet.

Q: Can I supply a list of ~100 SMARTS patterns (of unwanted moieties) to automatically mark/select/

May 30

May 20

How to update my PDB index to the latest one?

Q. How do I update my PDB index to the latest one? A. MolSoft updates the PDB index daily, but to

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How to update my PDB index to the latest one?

Q. How do I update my PDB index to the latest one? A. MolSoft updates the PDB index daily, but to

May 20

May 9

How to transfer and share docking hitlists.

Q: I created a hitlist under Windows and saved the project. When I open the ICM file on a Mac and

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How to transfer and share docking hitlists.

Q: I created a hitlist under Windows and saved the project. When I open the ICM file on a Mac and

May 9

May 9

Preserving Input SDF Metadata During Virtual Ligand Screening

Q1. How do I keep all metadata from my input SDF (eg, Catalog ID, PlateID, Well) in the docked

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Preserving Input SDF Metadata During Virtual Ligand Screening

Q1. How do I keep all metadata from my input SDF (eg, Catalog ID, PlateID, Well) in the docked

May 9

May 9

I'm trying to edit a peptide in the 3D Ligand Editor, but it's too large and won't load. What can I do?

Q. I'm trying to edit a peptide in the 3D Ligand Editor, but it's too large and won't

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I'm trying to edit a peptide in the 3D Ligand Editor, but it's too large and won't load. What can I do?

Q. I'm trying to edit a peptide in the 3D Ligand Editor, but it's too large and won't

May 9

May 1

How to undertake peptide docking to a receptor in ICM?

Q. How to undertake peptide docking to a receptor in ICM? A. Watch a video example here. To dock a

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How to undertake peptide docking to a receptor in ICM?

Q. How to undertake peptide docking to a receptor in ICM? A. Watch a video example here. To dock a

May 1

Apr 22

I see this message in my screening output file Loading ligand 446 Skipping 446 , estimated MW 525. > 500 - what does it mean?

Q. I see this message in my virtual ligand screening output file: Loading ligand 446 Skipping 446 ,

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I see this message in my screening output file Loading ligand 446 Skipping 446 , estimated MW 525. > 500 - what does it mean?

Q. I see this message in my virtual ligand screening output file: Loading ligand 446 Skipping 446 ,

Apr 22

Andrew Orry, Ruben2

Apr 19

How to assign a column as the name of a compound in an sdf export?

That was a good recipe. In simple terms, keep in mind the following 1) the molecular name in a

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How to assign a column as the name of a compound in an sdf export?

That was a good recipe. In simple terms, keep in mind the following 1) the molecular name in a

Apr 19

Apr 2

Q: How can I perform Free Wilson Regression Analysis in MolSoft's ICM-Pro?

Q: How can I perform Free Wilson Regression Analysis in MolSoft's ICM-Pro? A: To perform Free

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Q: How can I perform Free Wilson Regression Analysis in MolSoft's ICM-Pro?

Q: How can I perform Free Wilson Regression Analysis in MolSoft's ICM-Pro? A: To perform Free

Apr 2

Apr 2

How do I use Multi-Parameter Optimization (MPO) for binary classification in MolSoft's ICM-Pro?

Q How do I use Multi-Parameter Optimization (MPO) for binary classification in MolSoft's ICM-Pro?

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How do I use Multi-Parameter Optimization (MPO) for binary classification in MolSoft's ICM-Pro?

Q How do I use Multi-Parameter Optimization (MPO) for binary classification in MolSoft's ICM-Pro?

Apr 2

Apr 2

How to Score a hitlist from RIDGE using the Physics Based Score?

Q I have finished a RIDGE screen and it is scored using the neural network RTCNN score. How to score

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How to Score a hitlist from RIDGE using the Physics Based Score?

Q I have finished a RIDGE screen and it is scored using the neural network RTCNN score. How to score

Apr 2

Andrew Orry, Ruben2

Mar 10

I want to create a GUI dialog box in ICM for my bench chemists to use to retrieve chemicals by entering the ID number. How to create GUI popup dialogs?

A good question. The answer depends on the environment. When your chemists open ICM what do they see

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I want to create a GUI dialog box in ICM for my bench chemists to use to retrieve chemicals by entering the ID number. How to create GUI popup dialogs?

A good question. The answer depends on the environment. When your chemists open ICM what do they see

Mar 10

Andrew Orry, Ruben2

Mar 10

How to understand the color scheme in a sequence alignment?

If you want to know where does the Color-by menu in the alignment comes from, check the

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How to understand the color scheme in a sequence alignment?

If you want to know where does the Color-by menu in the alignment comes from, check the

Mar 10

Andrew Orry, Ruben2

Feb 23

How to locate gaps in a protein chain and cap them.

That works. Indeed, Select( a_A delete ). (or Select(a_A error )) function selects the boundary atoms

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How to locate gaps in a protein chain and cap them.

That works. Indeed, Select( a_A delete ). (or Select(a_A error )) function selects the boundary atoms

Feb 23

Feb 22

How to mutate multiple residues to Ala.

Q. How to mutate multiple residues to Ala. A. You can do this on the command line or in GUI. In both

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How to mutate multiple residues to Ala.

Q. How to mutate multiple residues to Ala. A. You can do this on the command line or in GUI. In both

Feb 22

Feb 11

Sharing a script smiles -> to 2D -> protonate -> generate 3D conformers -> mol2

Sharing a script—please feel free to adapt it to your needs or suggest improvements. This script

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Sharing a script smiles -> to 2D -> protonate -> generate 3D conformers -> mol2

Sharing a script—please feel free to adapt it to your needs or suggest improvements. This script

Feb 11

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