MolAICal
commented
1 year ago Please see your results:
Lowest affinity: 0.11 kcal/mol;
Highest affinity: 4.01 kcal/mol;
Average affinity: 1.10 kcal/mol;The lowest affinity is not negative. It seems that it does not generate the good ligands. Please check:
1) Is the selected center point in the receptor pocket? And are the box lengths suitable?
2) Some pockets of receptors are narrow. The quantity and diversity of growth fragments are not enough. Please use Pymol or ucsf chimera to check the pocket of the receptor. If the pocket seems to be narrow when initial fragment is located in the pocket, it will not have population generation because there is no space for fragment growth.
3) At last, if you want to get results, you can increase the cutoff value for selection. Modify parameters in configure file such as "InputParFileAI.dat":
selBindingScore -3
to
selBindingScore 3
xy127
It was not killed by me. 
Hello,
I set up my system and procedure same as tutorial. (protein and initial fragment is different) But after the run finished, there is no Results folder. I did get some files produced: vmdGen.tcl, MAICGrid.dat, tmpLigands.mol2, and denovo.log. temLigands.mol2 contains 2900 molecules, mostly fragments.
denovo.log prints
`# Project leader: Qifeng Bai, the official site of MolAICal: https://molaical.github.io or https://molaical.gitee.io #
Now generate Grids...... Now read atom, bond, etc parameters...... Total read fragments: 67. Now read generated Grids...... Now initial starting fragment...... 0 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading global configuration 4 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading defaults: jar:file:/home/ubuntu/user_space/MolAICal-linux64/MolAICal_lib/cdk-2.1.1.jar!/META-INF/jnati/jnati.default-properties 5 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact configuration: jniinchi-1.03_1 6 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults: jar:file:/home/ubuntu/user_space/MolAICal-linux64/MolAICal_lib/cdk-2.1.1.jar!/META-INF/jnati/jnati.instance.default-properties 8 [main] INFO net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath for: jniinchi-1.03_1-LINUX-AMD64 10 [main] INFO net.sf.jnati.deploy.repository.LocalRepository - Searching local repository for: jniinchi-1.03_1-LINUX-AMD64 10 [main] DEBUG net.sf.jnati.deploy.repository.LocalRepository - Artefact path: /home/ubuntu/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 11 [main] INFO net.sf.jnati.deploy.artefact.ManifestReader - Reading manifest 36 [main] INFO net.sf.jnati.deploy.NativeArtefactLocator - Artefact (jniinchi-1.03_1-LINUX-AMD64) location: /home/ubuntu/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 36 [main] DEBUG net.sf.jnati.deploy.NativeLibraryLoader - Loading library: /home/ubuntu/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64/libJniInchi-1.03_1-LINUX-AMD64.so ################################################################# Pop size: 119 Minimum molecular weight: 60; Maximum molecular weight: 252; Average molecular weight: 142; Lowest affinity: 0.11 kcal/mol; Highest affinity: 1.92 kcal/mol; Average affinity: 0.84 kcal/mol; ################################################################# The 1th cycle start at: 16:11:35 2023-04-20 Top 119 root ligands are chosen. Top 11 elite ligands are chosen. ################################################################# Pop size: 2567 Minimum molecular weight: 60; Maximum molecular weight: 431; Average molecular weight: 217; Lowest affinity: 0.11 kcal/mol; Highest affinity: 3.06 kcal/mol; Average affinity: 1.28 kcal/mol; ################################################################# Storing the 1th cycle result...... The 2th cycle start at: 17:13:29 2023-04-20 Top 200 root ligands are chosen. Top 256 elite ligands are chosen. ################################################################# Pop size: 2265 Minimum molecular weight: 60; Maximum molecular weight: 518; Average molecular weight: 215; Lowest affinity: 0.11 kcal/mol; Highest affinity: 4.01 kcal/mol; Average affinity: 1.10 kcal/mol; ################################################################# Storing the 2th cycle result...... '
Where is the problem?