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New commands and Functionalities

The version 2.0 of psfgen was extensively modified and improved to meet the current standards in the size of the structures, and the modern versions of additive CHARMM force field, and polarizable DRUDE force field (http://mackerell.umaryland.edu/charmm_ff.shtml).

New functionalities include:

To use the Drude force field, one only needs to load the Drude topology files and prepare the structures as per usual. Most commands are available for both lone pairs in the additive and polarizable force fields, although some operations are not yet available for Drude particles. Atom modification operations, e.g., psfset, and queries with the segment command on the drude particles, are not implemented. We advise the user to use VMD to assign beta and occupancy values during the structure preparation. writemol and readmol commands are not compatible with structure preparation for Drude Force field.

The new psfgen log file allows the user to save all the information regularly printed out during a psfgen execution script to a file. It is possible to open and close multiple log files in a psfgen script, but only one file is active at any given moment. An example of an application of multiple log files is to save the information of the loading process of the topology files to one log file and the rest of information of structure preparation to another file, as demonstrated below:

psfgen_logfile "load_topoplogy.log" 

topology top_all22_prot.rtf	
topology top_all36_carb.rtf	
topology top_all36_lipid.rtf	
topology top_all36_prot.rtf	
topology top_all36_cgenff.rtf	
topology toppar_water_ions.str

psfgen_logfile close

psfgen_logfile "structure_preparation.log" 

segment BPTI {
 pdb output/6PTI_protein.pdb
}

patch DISU BPTI:5 BPTI:55
patch DISU BPTI:14 BPTI:38
patch DISU BPTI:30 BPTI:51

pdbalias atom ILE CD1 CD
coordpdb output/6PTI_protein.pdb BPTI

pdbalias residue HOH TIP3  
segment SOLV {
 auto none
 pdb output/6PTI_water.pdb
}

pdbalias atom HOH O OH2
coordpdb output/6PTI_water.pdb SOLV

guesscoord

writepsf output/bpti.psf
writepdb output/bpti.pdb

psfgen_logfile close

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Next: Ordinary Usage Up: Creating PSF Structure Files Previous: Creating PSF Structure Files   Contents   Index
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