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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Received on Wed Oct 02 2019 - 17:30:02 PDT
