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#7629 07/29/05 10:25 PM
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CHChang Offline OP
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I am trying to create a dihedral basis to read in to REDU. I'm assuming the output of a "BASIS IC DIHEDRAL" command can be written to some kind of file, which will consist of dihedral angles to be read into REDU.

I have a PSF file, which should implicitly contain the sequence data for the system. When I read this in, along with the topology and parameter files, "IC FILL" gives message "FILLIC called with a null IC table", and PRINT IC shows NUMBER OF INTERNAL COORDINATES: 0". How is this table filled exactly? Does the system have to be built from scratch every time a job is run?


Christopher H. Chang, Ph.D. Research Associate, Computational Sciences National Renewable Energy Laboratory 1617 Cole Blvd., Mail Stop 1608 Golden, CO 80401
CHChang #7630 07/29/05 10:59 PM
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rmv Offline
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The IC table is a separate data structure, created via the SETUP option of the GENERATE command; it can be saved to a file for later use. It is initially filled with default data from the topology file, so for a structure with Cartesian coords, I suggest something like

gener a setup
ic purge
ic param
ic fill
open unit 2 write card name prot.ic
write ic unit 2 card
* initial ic table
*

I do not recommend the use of IC GENERate.

The VIBRAN docs aren't that clear about how to save the results of the BASIS command; other posts indicate that BASIS followed by WRITE NORM doesn't seem to work, but there's no clear explanation of what does work.


Rick Venable
computational chemist

rmv #7631 08/03/05 05:48 PM
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CHChang Offline OP
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Thanks very much, Rick. The docs for GENE do say:
"This command uses the sequence of residues specified in the last READ SEQUuence command and the information stored in the residue topology file to add the next segment to the PSF."

so it appears I must have the READ SEQU commands in there, and must regenerate what is already in the previously generated PSF file implicitly. Oh well.

For the record, the following VIBRAN block generates a dihedral basis and writes out to a file:

! Generate basis set of dihedral angles only.
VIBRAN ELEC ATOM FSWITCH CDIE -
VDW VATOM VSWITCHED -
CUTNB 12 CTOFNB 11 CTONNB 10 WMIN 1.5 EPS 1.0 -
NMODe 17641
BASIS IC DIHEdral

! Write out normal mode basis
OPEN UNIT 51 WRITE CARD NAME TEST.IC
WRITE NORM CARD UNIT 51
CLOSE UNIT 51

END


Christopher H. Chang, Ph.D. Research Associate, Computational Sciences National Renewable Energy Laboratory 1617 Cole Blvd., Mail Stop 1608 Golden, CO 80401

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