list gave me
> list
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY CHID
CHIE CHIP CHIS CILE CLEU CLYS CMET CPHE
CPRO CSER CTHR CTRP CTYR CVAL CYM CYS
CYX DA DA3 DA5 DAN DC DC3 DC5
DCN DG DG3 DG5 DGN DT DT3 DT5
DTN GLH GLN GLU GLY HID HIE HIP
HIS ILE LEU LYN LYS MET NALA NARG
NASN NASP NCYS NCYX NGLN NGLU NGLY NHE
NHID NHIE NHIP NHIS NILE NLEU NLYS NME
NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL
PARM99 PHE PRO SER THR TRP TYR VAL
c mods
>From the output
Loading PDB file: ./complex.pdb
total atoms in file: 22438
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY CHID
CHIE CHIP CHIS CILE CLEU CLYS CMET CPHE
CPRO CSER CTHR CTRP CTYR CVAL CYM CYS
CYX DA DA3 DA5 DAN DC DC3 DC5
DCN DG DG3 DG5 DGN DT DT3 DT5
DTN GLH GLN GLU GLY HID HIE HIP
HIS ILE LEU LYN LYS MET NALA NARG
NASN NASP NCYS NCYX NGLN NGLU NGLY NHE
NHID NHIE NHIP NHIS NILE NLEU NLYS NME
NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL
PARM99 PHE PRO SER THR TRP TYR VAL
c mods
addIons unit ion1 #ion1 [ion2 #ion2]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addIons, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
>From the input:
mods = loadamberparams frcmod.parmbsc1
c = loadpdb complex.pdb
list
#desc c
addIons c K+ 0 K 231 Cl 231
Thank you very much
krystyna
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Received on Mon Feb 05 2018 - 07:00:02 PST
