Dear Anselm,
I tried to set up the simulation with one MN and it is not giving any error
message. But when I tried this with four MN and with modified metals.prp
(added 3 more MN with coordinates) then it showed multiple errors (asking
for bond and torsion parameters). You can find my tleap input and errors
below.
tleap input: tleap.in
set default PBRadii mbondi2
source leaprc.protein.ff14SB
source leaprc.gaff2
loadoff ions94.lib
loadamberparams frcmod.ionsjc_tip3p
loadamberparams frcmod.vdWall
loadamberparams frcmod.constph
source leaprc.water.tip3p
loadAmberParams metals.dat
loadAmberPrep metals.prp
x = loadPDB new.pdb
saveAmberParm x stp_gas.parm7 stp_gas.rst7
savePdb x amb.pdb
solvatebox x TIP3PBOX 8
addions x NA 0
saveAmberParm x stp_wat.parm7 stp_wat.rst7
charge x
quit
*erros:*
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
Building angle parameters.
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find angle parameter: MN - MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find angle parameter: MN - MN - MN
Building proper torsion parameters.
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
** No torsion terms for MN-MN-MN-MN
Building improper torsion parameters.
total 788 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
Parameter file was not saved.
Writing pdb file: amb.pdb
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
Converting N-terminal residue name to PDB format: NMET -> MET
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
Converting C-terminal residue name to PDB format: CGLY -> GLY
Solute vdw bounding box: 48.251 123.586 209.116
Total bounding box for atom centers: 64.251 139.586 225.116
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 67.185 142.904 227.880 angstroms.
Volume: 2187880.029 A^3
Total mass 1150956.598 amu, Density 0.874 g/cc
Added 62336 residues.
5 NA ions required to neutralize.
Adding 5 counter ions to "x" using 1A grid
Grid extends from solute vdw + 1.37 to 7.37
Resolution: 1.00 Angstrom.
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
(No solvent overlap)
Placed NA in x at (-0.04, 38.58, 89.76).
(Replacing solvent molecule)
Placed NA in x at (-2.56, 36.54, 93.22).
(No solvent overlap)
Placed NA in x at (-11.04, 24.58, 64.76).
(No solvent overlap)
Placed NA in x at (-23.04, 33.58, 76.76).
(No solvent overlap)
Placed NA in x at (0.96, 30.58, 89.76).
Done adding ions.
Checking Unit.
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
There is a bond of 6.785308 angstroms between:
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
There is a bond of 7.211941 angstroms between:
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
There is a bond of 5.920439 angstroms between:
/home/dvsingh/softwares/amber18/bin/teLeap: Note.
Ignoring the warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find bond parameter for: MN - MN
Building angle parameters.
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find angle parameter: MN - MN - MN
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
Could not find angle parameter: MN - MN - MN
Building proper torsion parameters.
/home/dvsingh/softwares/amber18/bin/teLeap: Error!
** No torsion terms for MN-MN-MN-MN
Building improper torsion parameters.
total 788 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/home/dvsingh/softwares/amber18/bin/teLeap: Warning!
Parameter file was not saved.
Total unperturbed charge: -0.000000
Total perturbed charge: -0.000000
Quit
Exiting LEaP: Errors = 12; Warnings = 18; Notes = 3.
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Received on Thu Jan 06 2022 - 21:30:02 PST
