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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>
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Wed Oct 02 2019 - 07:00:03 PDT
