Dear Amber developers and users,
Thank you for usual kind support.
I am now trying to perform constant pH
MD.
‘leaprc.constph’ was loaded in LEaP
and
I just tried to save the parameter
files.
As the messages say, this leaprc file
includes
Several ions but the warning was
returned.
(The messages are shown below)
Loading parameters:
/home/kurisaki/amber/amber12/dat/leap/pa
rm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB +
frcmod.parmbsc0 + OL3 for RNA
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/amino10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/aminoct10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/aminont10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/phosphoaa10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/nucleic10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/ions08.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/solvents.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/constph.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/all_prot_nucleic10.lib
Loading library:
/home/kurisaki/amber/amber12/dat/leap/li
b/cph_nucleic_caps.lib
Loading parameters:
/home/kurisaki/amber/amber12/dat/leap/pa
rm/frcmod.constph
Reading force field modification type
file (frcmod)
Reading title:
Force field modifcations for
titrations
Loading parameters:
/home/kurisaki/amber/amber12/dat/leap/pa
rm/frcmod.protonated_nucleic
Reading force field modification type
file (frcmod)
Reading title:
Force field modifications for
protonated nucleic acids
Using H(N)-modified Bondi radii
Loading PDB file: ./test.pdb
total atoms in file: 4726
Leap added 5 missing atoms according
to residue templates:
5 H / lone pairs
Checking Unit.
WARNING: The unperturbed charge of the
unit: 5.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
For atom: .R<Na+ 296>.A<Na+ 1> Could
not find type: Na+
Parameter file was not saved.
Quit
(END)
This situation was not improved by
Loading leaprc.ff99SB, additionally.
I am most grateful if you tell me how to
Resolve this discrepancy.
Yours, sincerely.
Ikuo
Kurisaki
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Received on Sun Jul 08 2012 - 01:30:02 PDT
