CGenFFCaller plugin automates the fetching of CHARMM topology and parameters from the CGenFF server ( https://cgenff.umaryland.edu/).

Commands:

• cgenffcaller callcgenff -molfiles <List of Files> -username <CGenFF Username> -method <Fetching Tool>

  List of Options:

  • -molfiles <List of Files>: List of files to be submitted to CGenFF Server. Mol2 and PDB formats supported
  • -username <CGenFF Server Username>: CGenFF Server Account Username
  • -method <Web Server Fetching Tool>: Tool to use to fetch the information from the CGenFF Server.

    Note: The tool automatically select whatever is available. Linux and Mac use "wget" and "curl"; Windows machines use "curl" executed inside the powershell (Windows 10 only). This flag enforces the use the specified tool (for testing and debugging). A python script is executed if the mechanism mentioned so far fail. The last fall-back is to use the TCL packages HTTP and TLS, which their availability can not be guaranteed.

  Description:

  . Fetch the topology and parameters for the molecule files in the -molfiles list, and store them in a stream file (str). The stream files are stored internally, and can be accessed executing the command "callcgenff getstr <stream index>".

• cgenffcaller savemol -sel <atom selection object> -output <output file name> -format <file format: mol2, xyz, or pdb>

  Description:

  Save the the atom selection object (created using the "atomselect" command) to a file, and enforce the assignment of atoms' element as atoms' type to ensure compatibility with the CgenFF webserver. In the case of the mol2 file format, the bond order need to be set prior to the execution of the command.

• cgenffcaller numstr

  Description:

  Returns the number of stream files obtained from the CGenFF server.

• cgenffcaller getstr <index of the stream>

  Description:

  Returns the stream file stored at the index-th position. The indexes from 0 to [cgenffcaller numstr] -1 are valid. The order of the stream files follows the order of the "-molfiles" list option.

  "null" Result : A successful communication between VMD and CGenFF that didn't result in a stream file will return a "null" result.

• cgenffcaller getsubcount

  Description:

  Returns the number of submissions performed by the user. This command only works after the one submission had been performed.

Example

Assuming a list of molecule files a.pdb b.pdb c.mol2:

cgenffcaller callcgenff -molfiles {a.pdb b.pdb c.mol2} -username myusername

cgenffcaller numstr - This should return "3"

cgenffcaller getstr 0 - This should return the stream file for "a.pdb"

cgenffcaller getstr 1 - This should return the stream file for "b.pdb"

cgenffcaller getstr 2 - This should return the stream file for "c.pdb"

Contributors

• João Ribeiro, Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign