File Reading and Writing Opcodes
The opcodes in this section are linked below:
READ — READ a structure
Read a structure from the input file. Repeated READ commands read multiple structures from the input file.
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arg1 |
Molecular information retention |
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0 |
Default behavior |
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−1 |
Clear existing molecular information of previously read molecules and re-evaluate the substructure information. |
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This value is useful while using |
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−2 |
Clear existing molecular information of previously read molecules without re-evaluating the substructure information. |
WRIT — WRITe a structure
Writes the current structure to the output file. WRIT is not necessary for Monte Carlo searches and energy minimizations. It is used with molecular dynamics. Multiple WRIT statements put multiple structures into the output file.
TRED — Temporary file REaD
Reads a set of atomic coordinates from inname.tmp. This function is used to recover structures from a failed MULT or MCMM run or when MULT is set in a multiple-loop MacroModel command file. In the latter case, all loops after the first must use a TRED rather than a READ. With Version 4.5 and later, the need for this command should be minimal, since updates are now performed periodically during an MCMM search.
TOPN — Temporary file OPeN
Opens the temporary coordinate file filename.tmp, where filename is the stem of the input file name. This command is typically used to recover the structures saved during a failed MULT or MCMM run by combining the atom connection table from the input file and atomic coordinates from the .tmp file. A typical recovery command file is:
filename.mae filename-out.mae DEBG 1 READTOPN 100 BGINTREDWRITEND
This command file opens the filename.mae structure file and the filename.tmp temporary file, reads in the first 100 coordinate sets from the temporary file, and writes the corresponding structures to the output structure file, filename-out.mae. Arg1 of TOPN is the number of structures to be read from the temporary file. See the end of the failed job log file to find this number; however, be aware that the last structure in the .tmp file may be corrupted, depending on the nature of the failure of the previous job.
If this operation is to be used to recover structures from a run which used the SUBS command, then the SUBS commands in the original run must be included immediately after the READ command in the command list above.
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arg1 |
Number of atomic coordinate sets to be read from the .tmp file |