As of AmberTools 17 ion parameters are loaded along with water leaprc
files. It seems like you haven't loaded a water model so you have no
ion parameters. You need to have something like 'source
leaprc.water.tip3p' in your leap script. I highly recommend reading
the forcefield/LEaP sections of the Amber manual to become more
familiar with constructing systems in Amber. Hope this helps,
-Dan
On Mon, Feb 5, 2018 at 9:46 AM, Krystyna Zakrzewska <zakrze.icloud.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 06 2018 - 07:00:02 PST
