Hi,
I did look at the PDB file, and there is not any salt. Also, "addions" and
"addions2" work but take a longer time.
Best
On Wed, Oct 2, 2019 at 8:11 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> Simple test:
>
> addIonsRand mol Na+ 138
> addIonsRand mol K+ 456
> addIonsRand mol Cl- 456
>
> saveamberparm mol 1KX5-ED21A-iodFF-KCL-Na-SLTCAP.top
> 1KX5-ED21A-iodFF-KCL-Na-SLTCAP.crd
>
> $ grep "K+" 1KX5-ED21A-iodFF-KCL-Na-SLTCAP.top | head
>
> to see if the residues are in the prmtop.
>
> Bill
>
> On 10/2/19 6:59 AM, Parviz Seifpanahi Shabane wrote:
> > Thank you, for replying. This my whole script:
> >
> =================================================================================
> > source /usr/local/amber18/dat/leap/cmd/oldff/leaprc.ff99SB
> > set default PBradii bondi
> > WAT=OPC
> > mods = loadAmberParams parmBSC1.lib
> > mods = loadAmberParams frcmod.opc
> > mods = loadAmberParams frcmod.ions1lm_126_iod_opc
> > mol = loadpdb PDB-res85-Original-Implicit.pdb
> >
> > #addions mol Na+ 0
> > #addions mol Cl- 0
> >
> > solvateBox mol OPCBOX 21
> >
> > #addions2 mol Na+ 138
> > #addions2 mol K+ 459
> > #addions2 mol Cl- 459
> >
> > addIonsRand mol Na+ 138
> > addIonsRand mol K+ 456
> > addIonsRand mol Cl- 456
> >
> > saveamberparm mol 1KX5-ED21A-iodFF-KCL-Na-SLTCAP.top
> > 1KX5-ED21A-iodFF-KCL-Na-SLTCAP.crd
> > quit
> >
> ===================================================================================
> > So I do not think so the problem come from what Daniel said. I tried
> > different methods and different programes non of them showed the slat in
> > the systeam.
> > Best regards
> >
> > On Tue, Oct 1, 2019 at 9:07 PM David Case <david.case.rutgers.edu>
> wrote:
> >
> >> On Tue, Oct 01, 2019, Parviz Seifpanahi Shabane wrote:
> >>
> >>> Probelm is when I make PDB file fron file.crd and file.top by "ambpdb"
> >>> command I can not see any ions when I look at thesysteam by pymol or
> >> VMD!!!!
> >>> what is the probelm?
> >> Are the ions actually there in the PDB file? Sometimes the default
> >> options in a visualization program don't show ions.
> >>
> >> ....dac
> >>
> >>
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> >>
> >
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--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Fri Oct 04 2019 - 09:30:02 PDT
