Hello,
I discovered that if you use the check command on a unit which has some parameters missing, these parameters can be outputted to a parmset (check _unit_ _parmset_). I have tried this and it does say that the missing parameters have been saved.
> check Mod foo
Checking 'Mod'....
WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
Warning: Close contact of 1.308108 angstroms between .R<ASN 31>.A<HD22 12> and .R<GLN 33>.A<H 2>
Warning: Close contact of 1.306778 angstroms between .R<ASN 31>.A<HD21 11> and .R<TRP 34>.A<HD1 10>
Warning: Close contact of 1.447101 angstroms between .R<GLN 47>.A<HE21 14> and .R<ARG 49>.A<HH11 18>
Warning: Close contact of 1.365608 angstroms between .R<THR 80>.A<HG1 12> and .R<ASN 82>.A<H 2>
Warning: Close contact of 1.344597 angstroms between .R<ASN 82>.A<HD21 11> and .R<ASN 159>.A<HD22 12>
Warning: Close contact of 1.434957 angstroms between .R<ASN 83>.A<HD22 12> and .R<TYR 212>.A<HH 15>
Warning: Close contact of 1.480195 angstroms between .R<ARG 99>.A<HE 15> and .R<ARG 99>.A<H 2>
Warning: Close contact of 1.418586 angstroms between .R<ARG 99>.A<HD3 13> and .R<ARG 99>.A<HB3 7>
Warning: Close contact of 1.449587 angstroms between .R<SER 144>.A<HG 9> and .R<SER 147>.A<H 2>
Warning: Close contact of 0.544972 angstroms between .R<LYS 217>.A<HA 4> and .R<LYS 217>.A<CX 23>
Warning: Close contact of 0.001732 angstroms between .R<LYS 217>.A<HA 4> and .R<LYS 217>.A<HX1 24>
Warning: Close contact of 0.001732 angstroms between .R<LYS 217>.A<HA 4> and .R<LYS 217>.A<HX2 25>
Warning: Close contact of 0.003464 angstroms between .R<LYS 217>.A<HA 4> and .R<LYS 217>.A<HX3 26>
Warning: Close contact of 1.090495 angstroms between .R<LYS 217>.A<CA 3> and .R<LYS 217>.A<HX1 24>
Warning: Close contact of 1.089394 angstroms between .R<LYS 217>.A<CA 3> and .R<LYS 217>.A<HX2 25>
Warning: Close contact of 1.091049 angstroms between .R<LYS 217>.A<CA 3> and .R<LYS 217>.A<HX3 26>
Warning: Close contact of 0.003464 angstroms between .R<LYS 217>.A<HX1 24> and .R<LYS 217>.A<HX2 25>
Warning: Close contact of 0.001732 angstroms between .R<LYS 217>.A<HX1 24> and .R<LYS 217>.A<HX3 26>
Warning: Close contact of 0.005196 angstroms between .R<LYS 217>.A<HX2 25> and .R<LYS 217>.A<HX3 26>
Checking parameters for unit 'Mod'.
Creating empty parmset foo
Checking for bond parameters.
Could not find bond parameter for: CT - xx
Could not find bond parameter for: xx - zz
Could not find bond parameter for: xx - zz
Could not find bond parameter for: xx - zz
Checking for angle parameters.
Could not find angle parameter: C - CT - xx
Could not find angle parameter: CT - CT - xx
Could not find angle parameter: H1 - CT - xx
Could not find angle parameter: CT - xx - zz
Could not find angle parameter: CT - xx - zz
Could not find angle parameter: CT - xx - zz
Could not find angle parameter: N - CT - xx
Could not find angle parameter: zz - xx - zz
Could not find angle parameter: zz - xx - zz
Could not find angle parameter: zz - xx - zz
There are missing parameters.
Missing parameters have been added to the PARMSET.
check: Warnings: 20
Unit is OK.
However, when attempting to see or save the parmset, no command seems to work.
> desc foo
STRING (with no reference): 'foo'
> saveoff foo foo.frcmod
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage: saveOff <object> <filename>
These commands work fine and in the intended manner when used with existing parmsets (for example those loaded by the leaprc). What am I missing here? Why can't I see the parmset?
Kind regards
Pietro
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Received on Thu Aug 18 2016 - 02:00:08 PDT
