I docked a ligand (cellotetraose) to an enzyme using Scigress (Fujitsu). I saved the complex as pdb. Then, I created psf file using VEGA ZZ. However, when I solvate the complex using VMD, the console says solvation was successful, but I can’t get the water and the complex, it only shows the water molecules.
Please help.
Well, technically in the physical world when it's dissolved you don't see it anymore!!! The software program is pushed by AI artificial intelligence??? May/may not, at least to the dissolution state, although that's not the case!!! The problem lies, probably, in the interface between the software you are using for the modeling- changing from one to another! The incompatibility or limit exceeeding for the program may be other reason. (Please while posing your questions, use full details on the software/other modeling program with their differentiating characteristics since all the programs are not obvious and not universally used or generally practised. It's better to relate to well-known programs and versions! Thank You!).
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